Reference: https://thomaselove.github.io/2018-431-book/dataviz.html

Load packages

Load and read data

setwd('/Users/giovanna/Box/431_Denu_microbiome_metabolic_health')
pmrc <- read.csv("/Users/giovanna/Box/431_Denu_microbiome_metabolic_health/dr431_pmrc_20200403_with_formats_for_documentation.csv", na.strings = c("[. ] Missing"))
warrior <- read.csv("/Users/giovanna/Box/431_Denu_microbiome_metabolic_health/dr431_warrior_20190911_with_formats_for_documentation.csv", na.strings = c("[. ] Missing"))
spid <- read.csv("/Users/giovanna/Box/431_Denu_microbiome_metabolic_health/dr431_warrior_pmrc_spid_crosswalk.csv")
seq_id <- read.csv("/Users/giovanna/OneDrive - UW-Madison/Rotations/3 Denu-Rey/SHOW data/meta_data.csv")
table1.df <- dplyr::inner_join(seq_id, spid, by="NEW_ID")
table2.df <- dplyr::inner_join(table1.df, warrior, by="NEW_ID")
table3.df <- merge(table2.df, pmrc, by = "NEW_ID")
# table3.df contains PMRC subjects with their information from warrior and pmrc.

names(table3.df)[names(table3.df) == "index"] <- "16S_ID"

Create contingency table of gender, age, and seven indicatives for MetS

BMI (ANT_BMI); Triglycerides (PMRC_LAB_TRIG); HDL cholesterol (PMRC_LAB_HDLCHOL); Systolic BP (BP_SYSTOLIC_23); Diastolic BP (BP_DIASTOLIC_23); Glucose (PMRC_LAB_GLU), Hemoglobin 1ac (PMRC_LAB_GH); Waist Circumference (ANT_MEAS_WAIST_CM)

library(tidyverse)
## ── Attaching packages ──────────────────────────────────────────────────────────────── tidyverse 1.3.0 ──
## ✓ tibble  3.0.3     ✓ purrr   0.3.4
## ✓ tidyr   1.1.0     ✓ stringr 1.4.0
## ✓ readr   1.3.1     ✓ forcats 0.5.0
## ── Conflicts ─────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
## x dplyr::filter() masks stats::filter()
## x dplyr::lag()    masks stats::lag()
#library(dplyr)
MetS_feature <- table3.df %>%
             select("spid", "NEW_ID", "PMRC_ID","16S_ID", "ANT_BMI", "PMRC_LAB_TRIG","PMRC_LAB_HDLCHOL", "BP_SYSTOLIC_23", "BP_DIASTOLIC_23", "PMRC_LAB_GLU", "PMRC_LAB_GH", "GENDER", "AGE_CONSENT", "ANT_MEAS_WAIST_CM", "PMRC_FASTING_8HOURS")

mean(MetS_feature$AGE_CONSENT)
## [1] 57.23264
median(MetS_feature$AGE_CONSENT)
## [1] 61

A Subset: Fasting population

MetS_feature_fasting <- MetS_feature %>%
  filter(PMRC_FASTING_8HOURS == "[1] Yes") %>%
  select("spid","16S_ID", "ANT_BMI", "PMRC_LAB_TRIG","PMRC_LAB_HDLCHOL", "BP_SYSTOLIC_23", "BP_DIASTOLIC_23", "PMRC_LAB_GLU", "PMRC_LAB_GH", "GENDER", "AGE_CONSENT", "ANT_MEAS_WAIST_CM", "PMRC_FASTING_8HOURS") %>%
  na.omit
nrow(MetS_feature_fasting)
## [1] 81
# Among total of 288 plasma subjects, 81 have fasted

MetS_feature_fasting_female <- MetS_feature_fasting %>%
  filter(GENDER == "[2] Female") %>%
  select("spid","16S_ID", "ANT_BMI", "PMRC_LAB_TRIG","PMRC_LAB_HDLCHOL", "BP_SYSTOLIC_23", "BP_DIASTOLIC_23", "PMRC_LAB_GLU", "PMRC_LAB_GH", "GENDER", "AGE_CONSENT", "ANT_MEAS_WAIST_CM", "PMRC_FASTING_8HOURS") %>%
  na.omit
nrow(MetS_feature_fasting_female)
## [1] 51
# 51 out of 81 are fasted female

MetS_feature_fasting_male <- MetS_feature_fasting %>%
  filter(GENDER == "[1] Male") %>%
  select("spid","16S_ID", "ANT_BMI", "PMRC_LAB_TRIG","PMRC_LAB_HDLCHOL", "BP_SYSTOLIC_23", "BP_DIASTOLIC_23", "PMRC_LAB_GLU", "PMRC_LAB_GH", "GENDER", "AGE_CONSENT", "ANT_MEAS_WAIST_CM", "PMRC_FASTING_8HOURS") %>%
  na.omit
nrow(MetS_feature_fasting_male)
## [1] 30
# 30 out of 81 are fasted male

Diagnose subjects using NCEP ATP III’s MetS definition (doi: 10.1242/dmm.001180)

Waist Circumference over 102cm (men) or 89cm (women); bp over 130/85mmHg, fasting TG over 150mg/dL, fasting HDL cholesterol less than 40mg/dl (men) or 50mg/dl (women); fasting blood sugar over 100mg/dl

#Female
MetS_feature_female <- MetS_feature %>% filter(GENDER == "[2] Female")
bmi.binary <- ifelse(MetS_feature_fasting_female$ANT_BMI>=30,1,0)
sysbp.binary <- ifelse(MetS_feature_fasting_female$BP_SYSTOLIC_23>=130,1,0)
diabp.binary <- ifelse(MetS_feature_fasting_female$BP_DIASTOLIC_23>=85,1,0)
tg.binary <- ifelse(MetS_feature_fasting_female$PMRC_LAB_TRIG>=150,1,0)
hdl.binary <- ifelse(MetS_feature_fasting_female$PMRC_LAB_HDLCHOL<50,1,0)
glucose.binary <- ifelse(MetS_feature$PMRC_LAB_GLU>=100,1,0)

#Male
MetS_feature_male <- MetS_feature %>% filter(GENDER == "[1] Male")
bmi.binary <- ifelse(MetS_feature_fasting_male$ANT_BMI>=30,1,0)
sysbp.binary <- ifelse(MetS_feature_fasting_male$BP_SYSTOLIC_23>=130,1,0)
diabp.binary <- ifelse(MetS_feature_fasting_male$BP_DIASTOLIC_23>=85,1,0)
tg.binary <- ifelse(MetS_feature_fasting_male$PMRC_LAB_TRIG>=150,1,0)
hdl.binary <- ifelse(MetS_feature_fasting_male$PMRC_LAB_HDLCHOL<40,1,0)
glucose.binary <- ifelse(MetS_feature$PMRC_LAB_GLU>=100,1,0)


#HbA1C from all plasma subjects (both fasting and non-fasting); 1 = unhealthy
gh.binary <- ifelse(MetS_feature$PMRC_LAB_GH>6.5,1,0)

#If three or more criteria meet, then assigned to 1; otherwise 0 | (1 = unhealthy)
variable <- bmi.binary + sysbp.binary + diabp.binary + tg.binary + hdl.binary + glucose.binary
## Warning in bmi.binary + sysbp.binary + diabp.binary + tg.binary + hdl.binary + :
## longer object length is not a multiple of shorter object length
MetS.binary <- ifelse(variable>=3, 1, 0)

#Append gh.binary and MetS.binary to MetS_feature table
MetS_feature <- cbind(MetS_feature, gh.binary, MetS.binary)

#Combine MetS.binary and gh.binary for MetS; 0 = healthy; 1 = diseased
MetS_feature$MetS <- ifelse((MetS_feature$MetS.binary == 1) | (MetS_feature$gh.binary ==1), 1, 0)

#Number of diseased people in PMRC
diseased_PMRC <- MetS_feature %>%
  filter(MetS == "1") %>%
  select("spid", "MetS") %>%
  na.omit
nrow(diseased_PMRC)
## [1] 58
#58 have metabolic disease out of 288 PMRC people.

Correlation Test between age vs. phe

#male
MetS_feature_Male_num <- MetS_feature_male %>% select(-NEW_ID, -PMRC_ID, -`16S_ID`, -GENDER, -PMRC_FASTING_8HOURS) %>% na.omit
MetS_feature_Male_num <- as.data.frame(MetS_feature_Male_num)
cols <- t( combn(colnames(MetS_feature_Male_num),2) )
pvalue <- apply( cols , 1 , function(x) cor.test( MetS_feature_Male_num[,x[1] ] , MetS_feature_Male_num[ , x[2] ] )$p.value )
estimate <- apply( cols , 1 , function(x) cor.test( MetS_feature_Male_num[,x[1] ] , MetS_feature_Male_num[ , x[2] ] )$estimate )
cbind(cols,estimate,pvalue)
##                                              estimate             
##  [1,] "spid"             "ANT_BMI"           "0.0737676369000104" 
##  [2,] "spid"             "PMRC_LAB_TRIG"     "0.0703089070544183" 
##  [3,] "spid"             "PMRC_LAB_HDLCHOL"  "-0.343012730119083" 
##  [4,] "spid"             "BP_SYSTOLIC_23"    "0.30483218606412"   
##  [5,] "spid"             "BP_DIASTOLIC_23"   "0.0436452983236311" 
##  [6,] "spid"             "PMRC_LAB_GLU"      "0.0916168838459436" 
##  [7,] "spid"             "PMRC_LAB_GH"       "0.0994550047686194" 
##  [8,] "spid"             "AGE_CONSENT"       "0.240823211469777"  
##  [9,] "spid"             "ANT_MEAS_WAIST_CM" "0.0923926802675844" 
## [10,] "ANT_BMI"          "PMRC_LAB_TRIG"     "0.249677604887068"  
## [11,] "ANT_BMI"          "PMRC_LAB_HDLCHOL"  "-0.445807827764368" 
## [12,] "ANT_BMI"          "BP_SYSTOLIC_23"    "0.35016742845792"   
## [13,] "ANT_BMI"          "BP_DIASTOLIC_23"   "0.14246947201599"   
## [14,] "ANT_BMI"          "PMRC_LAB_GLU"      "0.317206607191021"  
## [15,] "ANT_BMI"          "PMRC_LAB_GH"       "0.467863818003446"  
## [16,] "ANT_BMI"          "AGE_CONSENT"       "0.140740854422792"  
## [17,] "ANT_BMI"          "ANT_MEAS_WAIST_CM" "0.925274822587552"  
## [18,] "PMRC_LAB_TRIG"    "PMRC_LAB_HDLCHOL"  "-0.427998632659358" 
## [19,] "PMRC_LAB_TRIG"    "BP_SYSTOLIC_23"    "0.144703464525829"  
## [20,] "PMRC_LAB_TRIG"    "BP_DIASTOLIC_23"   "0.084533925156262"  
## [21,] "PMRC_LAB_TRIG"    "PMRC_LAB_GLU"      "0.457035328239849"  
## [22,] "PMRC_LAB_TRIG"    "PMRC_LAB_GH"       "0.581611448143058"  
## [23,] "PMRC_LAB_TRIG"    "AGE_CONSENT"       "0.160145098779324"  
## [24,] "PMRC_LAB_TRIG"    "ANT_MEAS_WAIST_CM" "0.305380965191105"  
## [25,] "PMRC_LAB_HDLCHOL" "BP_SYSTOLIC_23"    "-0.187073692949041" 
## [26,] "PMRC_LAB_HDLCHOL" "BP_DIASTOLIC_23"   "0.00913657677625998"
## [27,] "PMRC_LAB_HDLCHOL" "PMRC_LAB_GLU"      "-0.297070230218143" 
## [28,] "PMRC_LAB_HDLCHOL" "PMRC_LAB_GH"       "-0.268873976863689" 
## [29,] "PMRC_LAB_HDLCHOL" "AGE_CONSENT"       "-0.273463820596766" 
## [30,] "PMRC_LAB_HDLCHOL" "ANT_MEAS_WAIST_CM" "-0.538359956384293" 
## [31,] "BP_SYSTOLIC_23"   "BP_DIASTOLIC_23"   "0.509709133353408"  
## [32,] "BP_SYSTOLIC_23"   "PMRC_LAB_GLU"      "0.0866752112578173" 
## [33,] "BP_SYSTOLIC_23"   "PMRC_LAB_GH"       "0.150461327216623"  
## [34,] "BP_SYSTOLIC_23"   "AGE_CONSENT"       "0.185717001029537"  
## [35,] "BP_SYSTOLIC_23"   "ANT_MEAS_WAIST_CM" "0.353448769342036"  
## [36,] "BP_DIASTOLIC_23"  "PMRC_LAB_GLU"      "-0.0892847794384579"
## [37,] "BP_DIASTOLIC_23"  "PMRC_LAB_GH"       "-0.225970504929801" 
## [38,] "BP_DIASTOLIC_23"  "AGE_CONSENT"       "-0.138191151450625" 
## [39,] "BP_DIASTOLIC_23"  "ANT_MEAS_WAIST_CM" "0.0937420587039849" 
## [40,] "PMRC_LAB_GLU"     "PMRC_LAB_GH"       "0.659985090135718"  
## [41,] "PMRC_LAB_GLU"     "AGE_CONSENT"       "0.287757875123229"  
## [42,] "PMRC_LAB_GLU"     "ANT_MEAS_WAIST_CM" "0.324563673059983"  
## [43,] "PMRC_LAB_GH"      "AGE_CONSENT"       "0.408673601513299"  
## [44,] "PMRC_LAB_GH"      "ANT_MEAS_WAIST_CM" "0.476900738936989"  
## [45,] "AGE_CONSENT"      "ANT_MEAS_WAIST_CM" "0.35583883262147"   
##       pvalue                
##  [1,] "0.63827347643845"    
##  [2,] "0.654141792073578"   
##  [3,] "0.0243344546303565"  
##  [4,] "0.046855678358561"   
##  [5,] "0.781088934018117"   
##  [6,] "0.559018402993811"   
##  [7,] "0.525735811918712"   
##  [8,] "0.119792755506533"   
##  [9,] "0.555680762367655"   
## [10,] "0.106377923474596"   
## [11,] "0.00273468407392845" 
## [12,] "0.0213376814367453"  
## [13,] "0.362102260933719"   
## [14,] "0.0382064488487508"  
## [15,] "0.00155799624669168" 
## [16,] "0.368015717770113"   
## [17,] "7.29661291568305e-19"
## [18,] "0.00419574406269305" 
## [19,] "0.354545436374883"   
## [20,] "0.589915875477805"   
## [21,] "0.00206318956412204" 
## [22,] "4.30752574388176e-05"
## [23,] "0.304968536028839"   
## [24,] "0.0464411217307064"  
## [25,] "0.229667506628989"   
## [26,] "0.953630541966013"   
## [27,] "0.053046759539573"   
## [28,] "0.081257525387583"   
## [29,] "0.0760009714729006"  
## [30,] "0.000196195713317478"
## [31,] "0.000480800947169436"
## [32,] "0.580495509259541"   
## [33,] "0.335514997058498"   
## [34,] "0.233124523814311"   
## [35,] "0.0200705091089707"  
## [36,] "0.569107647905036"   
## [37,] "0.145103670914154"   
## [38,] "0.376842976445718"   
## [39,] "0.549897869129921"   
## [40,] "1.47553589778814e-06"
## [41,] "0.0613249453850728"  
## [42,] "0.0337160117576358"  
## [43,] "0.00651200268786292" 
## [44,] "0.00122376459816195" 
## [45,] "0.0191878497108741"
#female
MetS_feature_Female_num <- MetS_feature_female %>% select(-NEW_ID, -PMRC_ID, -`16S_ID`, -GENDER, -PMRC_FASTING_8HOURS) %>% na.omit
MetS_feature_Female_num <- as.data.frame(MetS_feature_Female_num)
cols <- t( combn(colnames(MetS_feature_Female_num),2) )
pvalue <- apply( cols , 1 , function(x) cor.test( MetS_feature_Female_num[,x[1] ] , MetS_feature_Female_num[ , x[2] ] )$p.value )
estimate <- apply( cols , 1 , function(x) cor.test( MetS_feature_Female_num[,x[1] ] , MetS_feature_Female_num[ , x[2] ] )$estimate )
cbind(cols,estimate,pvalue)
##                                              estimate             
##  [1,] "spid"             "ANT_BMI"           "-0.0490427583449091"
##  [2,] "spid"             "PMRC_LAB_TRIG"     "-0.0944112129377198"
##  [3,] "spid"             "PMRC_LAB_HDLCHOL"  "0.0622980644953981" 
##  [4,] "spid"             "BP_SYSTOLIC_23"    "0.0605914162138858" 
##  [5,] "spid"             "BP_DIASTOLIC_23"   "0.00328530803093169"
##  [6,] "spid"             "PMRC_LAB_GLU"      "0.036438819737244"  
##  [7,] "spid"             "PMRC_LAB_GH"       "0.0912220453467413" 
##  [8,] "spid"             "AGE_CONSENT"       "0.0859660647544104" 
##  [9,] "spid"             "ANT_MEAS_WAIST_CM" "-0.102715034915411" 
## [10,] "ANT_BMI"          "PMRC_LAB_TRIG"     "0.190576307263433"  
## [11,] "ANT_BMI"          "PMRC_LAB_HDLCHOL"  "-0.36861192884788"  
## [12,] "ANT_BMI"          "BP_SYSTOLIC_23"    "0.0824274038762594" 
## [13,] "ANT_BMI"          "BP_DIASTOLIC_23"   "0.103886621055278"  
## [14,] "ANT_BMI"          "PMRC_LAB_GLU"      "0.337996569682703"  
## [15,] "ANT_BMI"          "PMRC_LAB_GH"       "0.364506113359263"  
## [16,] "ANT_BMI"          "AGE_CONSENT"       "0.0694134568915561" 
## [17,] "ANT_BMI"          "ANT_MEAS_WAIST_CM" "0.90596823426512"   
## [18,] "PMRC_LAB_TRIG"    "PMRC_LAB_HDLCHOL"  "-0.362820208315054" 
## [19,] "PMRC_LAB_TRIG"    "BP_SYSTOLIC_23"    "0.148148623830093"  
## [20,] "PMRC_LAB_TRIG"    "BP_DIASTOLIC_23"   "0.277727865526065"  
## [21,] "PMRC_LAB_TRIG"    "PMRC_LAB_GLU"      "0.176225697251854"  
## [22,] "PMRC_LAB_TRIG"    "PMRC_LAB_GH"       "0.0524044882573218" 
## [23,] "PMRC_LAB_TRIG"    "AGE_CONSENT"       "0.0542221007388887" 
## [24,] "PMRC_LAB_TRIG"    "ANT_MEAS_WAIST_CM" "0.229506685835264"  
## [25,] "PMRC_LAB_HDLCHOL" "BP_SYSTOLIC_23"    "0.0994153263448992" 
## [26,] "PMRC_LAB_HDLCHOL" "BP_DIASTOLIC_23"   "0.0567105534572735" 
## [27,] "PMRC_LAB_HDLCHOL" "PMRC_LAB_GLU"      "-0.234403515565394" 
## [28,] "PMRC_LAB_HDLCHOL" "PMRC_LAB_GH"       "-0.180901377298022" 
## [29,] "PMRC_LAB_HDLCHOL" "AGE_CONSENT"       "0.0460823648432636" 
## [30,] "PMRC_LAB_HDLCHOL" "ANT_MEAS_WAIST_CM" "-0.416629383061389" 
## [31,] "BP_SYSTOLIC_23"   "BP_DIASTOLIC_23"   "0.474545109863028"  
## [32,] "BP_SYSTOLIC_23"   "PMRC_LAB_GLU"      "-0.0258379850835637"
## [33,] "BP_SYSTOLIC_23"   "PMRC_LAB_GH"       "0.0897996897838481" 
## [34,] "BP_SYSTOLIC_23"   "AGE_CONSENT"       "0.408417683441886"  
## [35,] "BP_SYSTOLIC_23"   "ANT_MEAS_WAIST_CM" "0.05109681812577"   
## [36,] "BP_DIASTOLIC_23"  "PMRC_LAB_GLU"      "-0.0484249715768851"
## [37,] "BP_DIASTOLIC_23"  "PMRC_LAB_GH"       "-0.0834552927790453"
## [38,] "BP_DIASTOLIC_23"  "AGE_CONSENT"       "-0.163183000497014" 
## [39,] "BP_DIASTOLIC_23"  "ANT_MEAS_WAIST_CM" "0.0720319856308937" 
## [40,] "PMRC_LAB_GLU"     "PMRC_LAB_GH"       "0.844286527919386"  
## [41,] "PMRC_LAB_GLU"     "AGE_CONSENT"       "0.0654955052171833" 
## [42,] "PMRC_LAB_GLU"     "ANT_MEAS_WAIST_CM" "0.438200856627636"  
## [43,] "PMRC_LAB_GH"      "AGE_CONSENT"       "0.131646688272445"  
## [44,] "PMRC_LAB_GH"      "ANT_MEAS_WAIST_CM" "0.427389453483393"  
## [45,] "AGE_CONSENT"      "ANT_MEAS_WAIST_CM" "0.0449317554696872" 
##       pvalue                
##  [1,] "0.669818103369586"   
##  [2,] "0.410966529622175"   
##  [3,] "0.587925073968445"   
##  [4,] "0.598211801955012"   
##  [5,] "0.977226143231739"   
##  [6,] "0.751449734098696"   
##  [7,] "0.427019610727418"   
##  [8,] "0.454242559810132"   
##  [9,] "0.370852027188444"   
## [10,] "0.0946613014052198"  
## [11,] "0.000897960014677077"
## [12,] "0.473097688274793"   
## [13,] "0.365390696377115"   
## [14,] "0.00247388909084854" 
## [15,] "0.00103472072524153" 
## [16,] "0.545927098240874"   
## [17,] "4.27182636039728e-30"
## [18,] "0.00109615059750879" 
## [19,] "0.195511781459032"   
## [20,] "0.0138216733535293"  
## [21,] "0.122743208736308"   
## [22,] "0.648630977388502"   
## [23,] "0.637289273704681"   
## [24,] "0.0432497533193096"  
## [25,] "0.386498471975937"   
## [26,] "0.621896076027088"   
## [27,] "0.0388618869934056"  
## [28,] "0.112968525050499"   
## [29,] "0.688692179737485"   
## [30,] "0.00014811099138146" 
## [31,] "1.13695073524638e-05"
## [32,] "0.822330811858397"   
## [33,] "0.434293108478106"   
## [34,] "0.000205567035491337"
## [35,] "0.65684058363499"    
## [36,] "0.673740464938856"   
## [37,] "0.467577682205579"   
## [38,] "0.153431997826268"   
## [39,] "0.530847275543755"   
## [40,] "2.76231525177494e-22"
## [41,] "0.568871750350499"   
## [42,] "6.00776225052311e-05"
## [43,] "0.250593459267857"   
## [44,] "9.51517427989896e-05"
## [45,] "0.696080287728924"

Visualization - Scatter plot: Features vs Age by Gender; Using whole PMRC

#Divide the age into quantiles
agegroup_quantile <- quantile(MetS_feature$AGE_CONSENT, probs = seq(0,1,0.3333333), na.rm = TRUE, names = TRUE, type = 1)
agegroup_quantile
##        0% 33.33333% 66.66666% 99.99999% 
##        18        53        66        88
#age between 18-53: Young; 54-66: middle; 67-88: old

##Divide the agegroup by quantile
MetS_feature <- MetS_feature %>% mutate(ageGroup=case_when(
                                  AGE_CONSENT<=agegroup_quantile[2] ~ "young",
                                  AGE_CONSENT<=agegroup_quantile[3] ~ "middle",
                                  AGE_CONSENT<=agegroup_quantile[4] ~ "old"
))
##Plot the agegroup vs. phe
ggplot(MetS_feature,aes(x=AGE_CONSENT, y=ANT_BMI, color=ageGroup))+
  geom_point()
## Warning: Removed 3 rows containing missing values (geom_point).

ggplot(MetS_feature,aes(x=AGE_CONSENT, y=PMRC_LAB_TRIG, color=ageGroup))+
  geom_point()
## Warning: Removed 161 rows containing missing values (geom_point).

ggplot(MetS_feature,aes(x=AGE_CONSENT, y=PMRC_LAB_HDLCHOL, color=ageGroup))+
  geom_point()
## Warning: Removed 164 rows containing missing values (geom_point).

ggplot(MetS_feature,aes(x=AGE_CONSENT, y=BP_SYSTOLIC_23, color=ageGroup))+
  geom_point()
## Warning: Removed 2 rows containing missing values (geom_point).

ggplot(MetS_feature,aes(x=AGE_CONSENT, y=BP_DIASTOLIC_23, color=ageGroup))+
  geom_point()
## Warning: Removed 2 rows containing missing values (geom_point).

ggplot(MetS_feature,aes(x=AGE_CONSENT, y=PMRC_LAB_GLU, color=ageGroup))+
  geom_point()
## Warning: Removed 164 rows containing missing values (geom_point).

ggplot(MetS_feature,aes(x=AGE_CONSENT, y=PMRC_LAB_GH, color=ageGroup))+
  geom_point()
## Warning: Removed 164 rows containing missing values (geom_point).

ggplot(MetS_feature,aes(x=AGE_CONSENT, y=ANT_MEAS_WAIST_CM, color=ageGroup))+
  geom_point()

#PMRC_female

#Divide the age into quantiles
#female
agegroup_quantile <- quantile(MetS_feature_female$AGE_CONSENT, probs = seq(0,1,0.3333333), na.rm = TRUE, names = TRUE, type = 1)
agegroup_quantile
##        0% 33.33333% 66.66666% 99.99999% 
##        22        52        64        85
#age between 22-52: Young female; 53-64: middle female; 65-85: old female

##Assign the ageGroup for female
MetS_feature_female <- MetS_feature_female %>% mutate(ageGroup=case_when(
                                  AGE_CONSENT<=agegroup_quantile[2] ~ "young",
                                  AGE_CONSENT<=agegroup_quantile[3] ~ "middle",
                                  AGE_CONSENT<=agegroup_quantile[4] ~ "old"
))


#Plot the agegroup vs. phe for female
ggplot(MetS_feature_female,aes(x=AGE_CONSENT, y=ANT_BMI, color=ageGroup))+
  geom_point()
## Warning: Removed 2 rows containing missing values (geom_point).

ggplot(MetS_feature_female,aes(x=AGE_CONSENT, y=PMRC_LAB_TRIG, color=ageGroup))+
  geom_point()
## Warning: Removed 88 rows containing missing values (geom_point).

ggplot(MetS_feature_female,aes(x=AGE_CONSENT, y=PMRC_LAB_HDLCHOL, color=ageGroup))+
  geom_point()
## Warning: Removed 90 rows containing missing values (geom_point).

ggplot(MetS_feature_female,aes(x=AGE_CONSENT, y=BP_SYSTOLIC_23, color=ageGroup))+
  geom_point()
## Warning: Removed 1 rows containing missing values (geom_point).

ggplot(MetS_feature_female,aes(x=AGE_CONSENT, y=BP_DIASTOLIC_23, color=ageGroup))+
  geom_point()
## Warning: Removed 1 rows containing missing values (geom_point).

ggplot(MetS_feature_female,aes(x=AGE_CONSENT, y=PMRC_LAB_GLU, color=ageGroup))+
  geom_point()
## Warning: Removed 90 rows containing missing values (geom_point).

ggplot(MetS_feature_female,aes(x=AGE_CONSENT, y=PMRC_LAB_GH, color=ageGroup))+
  geom_point()
## Warning: Removed 90 rows containing missing values (geom_point).

ggplot(MetS_feature_female,aes(x=AGE_CONSENT, y=ANT_MEAS_WAIST_CM, color=ageGroup))+
  geom_point()

#Correlation Test by ageGroup
#ageGroup==young
MetS_feature_Female_ageGroup_young <- MetS_feature_female %>% select(-NEW_ID, -PMRC_ID, -`16S_ID`, -GENDER, -PMRC_FASTING_8HOURS, -ageGroup) %>% na.omit
MetS_feature_Female_ageGroup_young <- MetS_feature_female %>% filter(ageGroup=="young") %>% na.omit
MetS_feature_Female_ageGroup_young <- as.data.frame(MetS_feature_Female_ageGroup_young)

res.bmi <- cor.test(MetS_feature_Female_ageGroup_young$AGE_CONSENT, MetS_feature_Female_ageGroup_young$ANT_BMI, 
                    method = "pearson")
res.trig <- cor.test(MetS_feature_Female_ageGroup_young$PMRC_LAB_TRIG, MetS_feature_Female_ageGroup_young$PMRC_LAB_TRIG, 
                    method = "pearson")
res.hdl <- cor.test(MetS_feature_Female_ageGroup_young$PMRC_LAB_HDLCHOL, MetS_feature_Female_ageGroup_young$PMRC_LAB_HDLCHOL, 
                    method = "pearson")
res.sys <- cor.test(MetS_feature_Female_ageGroup_young$BP_SYSTOLIC_23, MetS_feature_Female_ageGroup_young$BP_SYSTOLIC_23, 
                    method = "pearson")
res.dias <- cor.test(MetS_feature_Female_ageGroup_young$BP_DIASTOLIC_23, MetS_feature_Female_ageGroup_young$BP_DIASTOLIC_23, 
                    method = "pearson")
res.glu <- cor.test(MetS_feature_Female_ageGroup_young$PMRC_LAB_GLU, MetS_feature_Female_ageGroup_young$PMRC_LAB_GLU, 
                    method = "pearson")
res.gh <- cor.test(MetS_feature_Female_ageGroup_young$PMRC_LAB_GH, MetS_feature_Female_ageGroup_young$PMRC_LAB_GH, 
                    method = "pearson")
res.waist <- cor.test(MetS_feature_Female_ageGroup_young$ANT_MEAS_WAIST_CM, MetS_feature_Female_ageGroup_young$ANT_MEAS_WAIST_CM, 
                    method = "pearson")


#ageGroup==middle
MetS_feature_Female_ageGroup_middle <- MetS_feature_female %>% select(-NEW_ID, -PMRC_ID, -`16S_ID`, -GENDER, -PMRC_FASTING_8HOURS, -ageGroup) %>% na.omit
MetS_feature_Female_ageGroup_middle <- MetS_feature_female %>% filter(ageGroup=="young") %>% na.omit
MetS_feature_Female_ageGroup_middle <- as.data.frame(MetS_feature_Female_ageGroup_middle)

res.bmi <- cor.test(MetS_feature_Female_ageGroup_middle$AGE_CONSENT, MetS_feature_Female_ageGroup_middle$ANT_BMI, 
                    method = "pearson")
res.trig <- cor.test(MetS_feature_Female_ageGroup_middle$PMRC_LAB_TRIG, MetS_feature_Female_ageGroup_middle$PMRC_LAB_TRIG, 
                    method = "pearson")
res.hdl <- cor.test(MetS_feature_Female_ageGroup_middle$PMRC_LAB_HDLCHOL, MetS_feature_Female_ageGroup_middle$PMRC_LAB_HDLCHOL, 
                    method = "pearson")
res.sys <- cor.test(MetS_feature_Female_ageGroup_middle$BP_SYSTOLIC_23, MetS_feature_Female_ageGroup_middle$BP_SYSTOLIC_23, 
                    method = "pearson")
res.dias <- cor.test(MetS_feature_Female_ageGroup_middle$BP_DIASTOLIC_23, MetS_feature_Female_ageGroup_middle$BP_DIASTOLIC_23, 
                    method = "pearson")
res.glu <- cor.test(MetS_feature_Female_ageGroup_middle$PMRC_LAB_GLU, MetS_feature_Female_ageGroup_middle$PMRC_LAB_GLU, 
                    method = "pearson")
res.gh <- cor.test(MetS_feature_Female_ageGroup_middle$PMRC_LAB_GH, MetS_feature_Female_ageGroup_middle$PMRC_LAB_GH, 
                    method = "pearson")
res.waist <- cor.test(MetS_feature_Female_ageGroup_middle$ANT_MEAS_WAIST_CM, MetS_feature_Female_ageGroup_middle$ANT_MEAS_WAIST_CM, 
                    method = "pearson")


#ageGroup==old
MetS_feature_Female_ageGroup_old <- MetS_feature_female %>% select(-NEW_ID, -PMRC_ID, -`16S_ID`, -GENDER, -PMRC_FASTING_8HOURS, -ageGroup) %>% na.omit
MetS_feature_Female_ageGroup_old <- MetS_feature_female %>% filter(ageGroup=="young") %>% na.omit
MetS_feature_Female_ageGroup_old <- as.data.frame(MetS_feature_Female_ageGroup_old)

res.bmi <- cor.test(MetS_feature_Female_ageGroup_old$AGE_CONSENT, MetS_feature_Female_ageGroup_old$ANT_BMI, 
                    method = "pearson")
res.trig <- cor.test(MetS_feature_Female_ageGroup_old$PMRC_LAB_TRIG, MetS_feature_Female_ageGroup_old$PMRC_LAB_TRIG, 
                    method = "pearson")
res.hdl <- cor.test(MetS_feature_Female_ageGroup_old$PMRC_LAB_HDLCHOL, MetS_feature_Female_ageGroup_old$PMRC_LAB_HDLCHOL, 
                    method = "pearson")
res.sys <- cor.test(MetS_feature_Female_ageGroup_old$BP_SYSTOLIC_23, MetS_feature_Female_ageGroup_old$BP_SYSTOLIC_23, 
                    method = "pearson")
res.dias <- cor.test(MetS_feature_Female_ageGroup_old$BP_DIASTOLIC_23, MetS_feature_Female_ageGroup_old$BP_DIASTOLIC_23, 
                    method = "pearson")
res.glu <- cor.test(MetS_feature_Female_ageGroup_old$PMRC_LAB_GLU, MetS_feature_Female_ageGroup_old$PMRC_LAB_GLU, 
                    method = "pearson")
res.gh <- cor.test(MetS_feature_Female_ageGroup_old$PMRC_LAB_GH, MetS_feature_Female_ageGroup_old$PMRC_LAB_GH, 
                    method = "pearson")
res.waist <- cor.test(MetS_feature_Female_ageGroup_old$ANT_MEAS_WAIST_CM, MetS_feature_Female_ageGroup_old$ANT_MEAS_WAIST_CM, 
                    method = "pearson")

#PMRC_male

#male
agegroup_quantile <- quantile(MetS_feature_male$AGE_CONSENT, probs = seq(0,1,0.3333333), na.rm = TRUE, names = TRUE, type = 1)
agegroup_quantile
##        0% 33.33333% 66.66666% 99.99999% 
##        18        53        68        88
#age between 26-55: Young male; 56-66: middle male; 67-82: old male

##Assign the ageGroup for male
MetS_feature_male <- MetS_feature_male %>% mutate(ageGroup=case_when(
                                  AGE_CONSENT<=agegroup_quantile[2] ~ "young",
                                  AGE_CONSENT<=agegroup_quantile[3] ~ "middle",
                                  AGE_CONSENT<=agegroup_quantile[4] ~ "old"
))

#Plot the agegroup vs. phe for male
ggplot(MetS_feature_male,aes(x=AGE_CONSENT, y=ANT_BMI, color=ageGroup))+
  geom_point()
## Warning: Removed 1 rows containing missing values (geom_point).

ggplot(MetS_feature_male,aes(x=AGE_CONSENT, y=PMRC_LAB_TRIG, color=ageGroup))+
  geom_point()
## Warning: Removed 73 rows containing missing values (geom_point).

ggplot(MetS_feature_male,aes(x=AGE_CONSENT, y=PMRC_LAB_HDLCHOL, color=ageGroup))+
  geom_point()
## Warning: Removed 74 rows containing missing values (geom_point).

ggplot(MetS_feature_male,aes(x=AGE_CONSENT, y=BP_SYSTOLIC_23, color=ageGroup))+
  geom_point()
## Warning: Removed 1 rows containing missing values (geom_point).

ggplot(MetS_feature_male,aes(x=AGE_CONSENT, y=BP_DIASTOLIC_23, color=ageGroup))+
  geom_point()
## Warning: Removed 1 rows containing missing values (geom_point).

ggplot(MetS_feature_male,aes(x=AGE_CONSENT, y=PMRC_LAB_GLU, color=ageGroup))+
  geom_point()
## Warning: Removed 74 rows containing missing values (geom_point).

ggplot(MetS_feature_male,aes(x=AGE_CONSENT, y=PMRC_LAB_GH, color=ageGroup))+
  geom_point()
## Warning: Removed 74 rows containing missing values (geom_point).

ggplot(MetS_feature_male,aes(x=AGE_CONSENT, y=ANT_MEAS_WAIST_CM, color=ageGroup))+
  geom_point()

#Correlation Test by ageGroup
#ageGroup==young
MetS_feature_Male_ageGroup_young <- MetS_feature_male %>% select(-NEW_ID, -PMRC_ID, -`16S_ID`, -GENDER, -PMRC_FASTING_8HOURS, -ageGroup) %>% na.omit
MetS_feature_Male_ageGroup_young <- MetS_feature_male %>% filter(ageGroup=="young") %>% na.omit
MetS_feature_Male_ageGroup_young <- as.data.frame(MetS_feature_Male_ageGroup_young)

res.bmi <- cor.test(MetS_feature_Male_ageGroup_young$AGE_CONSENT, MetS_feature_Male_ageGroup_young$ANT_BMI, 
                    method = "pearson")
res.trig <- cor.test(MetS_feature_Male_ageGroup_young$PMRC_LAB_TRIG, MetS_feature_Male_ageGroup_young$PMRC_LAB_TRIG, 
                    method = "pearson")
res.hdl <- cor.test(MetS_feature_Male_ageGroup_young$PMRC_LAB_HDLCHOL, MetS_feature_Male_ageGroup_young$PMRC_LAB_HDLCHOL, 
                    method = "pearson")
res.sys <- cor.test(MetS_feature_Male_ageGroup_young$BP_SYSTOLIC_23, MetS_feature_Male_ageGroup_young$BP_SYSTOLIC_23, 
                    method = "pearson")
res.dias <- cor.test(MetS_feature_Male_ageGroup_young$BP_DIASTOLIC_23, MetS_feature_Male_ageGroup_young$BP_DIASTOLIC_23, 
                    method = "pearson")
res.glu <- cor.test(MetS_feature_Male_ageGroup_young$PMRC_LAB_GLU, MetS_feature_Male_ageGroup_young$PMRC_LAB_GLU, 
                    method = "pearson")
res.gh <- cor.test(MetS_feature_Male_ageGroup_young$PMRC_LAB_GH, MetS_feature_Male_ageGroup_young$PMRC_LAB_GH, 
                    method = "pearson")
res.waist <- cor.test(MetS_feature_Male_ageGroup_young$ANT_MEAS_WAIST_CM, MetS_feature_Male_ageGroup_young$ANT_MEAS_WAIST_CM, 
                    method = "pearson")


#ageGroup==middle
MetS_feature_Male_ageGroup_middle <- MetS_feature_male %>% select(-NEW_ID, -PMRC_ID, -`16S_ID`, -GENDER, -PMRC_FASTING_8HOURS, -ageGroup) %>% na.omit
MetS_feature_Male_ageGroup_middle <- MetS_feature_male %>% filter(ageGroup=="young") %>% na.omit
MetS_feature_Male_ageGroup_middle <- as.data.frame(MetS_feature_Male_ageGroup_middle)

res.bmi <- cor.test(MetS_feature_Male_ageGroup_middle$AGE_CONSENT, MetS_feature_Male_ageGroup_middle$ANT_BMI, 
                    method = "pearson")
res.trig <- cor.test(MetS_feature_Male_ageGroup_middle$PMRC_LAB_TRIG, MetS_feature_Male_ageGroup_middle$PMRC_LAB_TRIG, 
                    method = "pearson")
res.hdl <- cor.test(MetS_feature_Male_ageGroup_middle$PMRC_LAB_HDLCHOL, MetS_feature_Male_ageGroup_middle$PMRC_LAB_HDLCHOL, 
                    method = "pearson")
res.sys <- cor.test(MetS_feature_Male_ageGroup_middle$BP_SYSTOLIC_23, MetS_feature_Male_ageGroup_middle$BP_SYSTOLIC_23, 
                    method = "pearson")
res.dias <- cor.test(MetS_feature_Male_ageGroup_middle$BP_DIASTOLIC_23, MetS_feature_Male_ageGroup_middle$BP_DIASTOLIC_23, 
                    method = "pearson")
res.glu <- cor.test(MetS_feature_Male_ageGroup_middle$PMRC_LAB_GLU, MetS_feature_Male_ageGroup_middle$PMRC_LAB_GLU, 
                    method = "pearson")
res.gh <- cor.test(MetS_feature_Male_ageGroup_middle$PMRC_LAB_GH, MetS_feature_Male_ageGroup_middle$PMRC_LAB_GH, 
                    method = "pearson")
res.waist <- cor.test(MetS_feature_Male_ageGroup_middle$ANT_MEAS_WAIST_CM, MetS_feature_Male_ageGroup_middle$ANT_MEAS_WAIST_CM, 
                    method = "pearson")


#ageGroup==old
MetS_feature_Male_ageGroup_old <- MetS_feature_male %>% select(-NEW_ID, -PMRC_ID, -`16S_ID`, -GENDER, -PMRC_FASTING_8HOURS, -ageGroup) %>% na.omit
MetS_feature_Male_ageGroup_old <- MetS_feature_male %>% filter(ageGroup=="young") %>% na.omit
MetS_feature_Male_ageGroup_old <- as.data.frame(MetS_feature_Male_ageGroup_old)

res.bmi <- cor.test(MetS_feature_Male_ageGroup_old$AGE_CONSENT, MetS_feature_Male_ageGroup_old$ANT_BMI, 
                    method = "pearson")
res.trig <- cor.test(MetS_feature_Male_ageGroup_old$PMRC_LAB_TRIG, MetS_feature_Male_ageGroup_old$PMRC_LAB_TRIG, 
                    method = "pearson")
res.hdl <- cor.test(MetS_feature_Male_ageGroup_old$PMRC_LAB_HDLCHOL, MetS_feature_Male_ageGroup_old$PMRC_LAB_HDLCHOL, 
                    method = "pearson")
res.sys <- cor.test(MetS_feature_Male_ageGroup_old$BP_SYSTOLIC_23, MetS_feature_Male_ageGroup_old$BP_SYSTOLIC_23, 
                    method = "pearson")
res.dias <- cor.test(MetS_feature_Male_ageGroup_old$BP_DIASTOLIC_23, MetS_feature_Male_ageGroup_old$BP_DIASTOLIC_23, 
                    method = "pearson")
res.glu <- cor.test(MetS_feature_Male_ageGroup_old$PMRC_LAB_GLU, MetS_feature_Male_ageGroup_old$PMRC_LAB_GLU, 
                    method = "pearson")
res.gh <- cor.test(MetS_feature_Male_ageGroup_old$PMRC_LAB_GH, MetS_feature_Male_ageGroup_old$PMRC_LAB_GH, 
                    method = "pearson")
res.waist <- cor.test(MetS_feature_Male_ageGroup_old$ANT_MEAS_WAIST_CM, MetS_feature_Male_ageGroup_old$ANT_MEAS_WAIST_CM, 
                    method = "pearson")

#Multicorr test with taxa # Correlation test between each phenotype and age in male

res.bmi <- cor.test(MetS_feature_male$AGE_CONSENT, MetS_feature_male$ANT_BMI, 
                    method = "pearson")

res.trig <- cor.test(MetS_feature_male$PMRC_LAB_TRIG, MetS_feature_male$PMRC_LAB_TRIG, 
                    method = "pearson")

res.hdl <- cor.test(MetS_feature_male$PMRC_LAB_HDLCHOL, MetS_feature_male$PMRC_LAB_HDLCHOL, 
                    method = "pearson")

res.sys <- cor.test(MetS_feature_male$BP_SYSTOLIC_23, MetS_feature_male$BP_SYSTOLIC_23, 
                    method = "pearson")

res.dias <- cor.test(MetS_feature_male$BP_DIASTOLIC_23, MetS_feature_male$BP_DIASTOLIC_23, 
                    method = "pearson")

res.glu <- cor.test(MetS_feature_male$PMRC_LAB_GLU, MetS_feature_male$PMRC_LAB_GLU, 
                    method = "pearson")

res.gh <- cor.test(MetS_feature_male$PMRC_LAB_GH, MetS_feature_male$PMRC_LAB_GH, 
                    method = "pearson")

res.waist <- cor.test(MetS_feature_male$ANT_MEAS_WAIST_CM, MetS_feature_male$ANT_MEAS_WAIST_CM, 
                    method = "pearson")

Correlation test between each phenotype and age in female

res.bmi <- cor.test(MetS_feature_female$AGE_CONSENT, MetS_feature_female$ANT_BMI, 
                    method = "pearson")

res.trig <- cor.test(MetS_feature_female$PMRC_LAB_TRIG, MetS_feature_female$PMRC_LAB_TRIG, 
                    method = "pearson")

res.hdl <- cor.test(MetS_feature_female$PMRC_LAB_HDLCHOL, MetS_feature_female$PMRC_LAB_HDLCHOL, 
                    method = "pearson")

res.sys <- cor.test(MetS_feature_female$BP_SYSTOLIC_23, MetS_feature_female$BP_SYSTOLIC_23, 
                    method = "pearson")

res.dias <- cor.test(MetS_feature_female$BP_DIASTOLIC_23, MetS_feature_female$BP_DIASTOLIC_23, 
                    method = "pearson")

res.glu <- cor.test(MetS_feature_female$PMRC_LAB_GLU, MetS_feature_female$PMRC_LAB_GLU, 
                    method = "pearson")

res.gh <- cor.test(MetS_feature_female$PMRC_LAB_GH, MetS_feature_female$PMRC_LAB_GH, 
                    method = "pearson")

res.waist <- cor.test(MetS_feature_female$ANT_MEAS_WAIST_CM, MetS_feature_female$ANT_MEAS_WAIST_CM, 
                    method = "pearson")

#Read dataframes_level2_Phylums

#ASVs <- read_qza("microbiome_data/filtered/table_filt.qza") #Gives me an error so I commented out.
taxa_table <- read.csv("level-2_phylum_taxtable_clean.csv", header=T)
taxa_table = taxa_table[,1:13] #all rows, from columns 1 to 13
taxa_ra <- sweep(taxa_table[,2:ncol(taxa_table)],1,rowSums(taxa_table[,2:ncol(taxa_table)]),"/") #relative abundance - normalization of sample reads
taxa_ra$index = taxa_table$index
merged.table_phylum <- merge(MetS_feature, taxa_ra, by.x="16S_ID", by.y="index")


merged.table_male <- merged.table_phylum %>%
  filter(GENDER == "[1] Male")
merged.table_female <- merged.table_phylum %>%
  filter(GENDER == "[2] Female")

#Regression
MetS_feature$MetS <- ifelse((MetS_feature$MetS.binary == 1) | (MetS_feature$gh.binary ==1), 1, 0)
reg_data_phylum <- merged.table_phylum %>% select(MetS,AGE_CONSENT, ANT_BMI, PMRC_LAB_TRIG, PMRC_LAB_HDLCHOL, BP_SYSTOLIC_23, BP_DIASTOLIC_23, PMRC_LAB_GLU, PMRC_LAB_GH, ANT_MEAS_WAIST_CM, starts_with("D_0__"))
lmod <- glm(MetS ~ ., family = "binomial", data = reg_data_phylum)
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
summary(lmod)
## 
## Call:
## glm(formula = MetS ~ ., family = "binomial", data = reg_data_phylum)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -1.7910  -0.9004  -0.1359   0.7894   2.1031  
## 
## Coefficients: (1 not defined because of singularities)
##                                         Estimate Std. Error z value Pr(>|z|)  
## (Intercept)                            1.662e+01  1.619e+01   1.026   0.3048  
## AGE_CONSENT                           -3.450e-02  2.084e-02  -1.656   0.0978 .
## ANT_BMI                                2.894e-02  7.601e-02   0.381   0.7034  
## PMRC_LAB_TRIG                          3.692e-03  3.423e-03   1.079   0.2808  
## PMRC_LAB_HDLCHOL                      -1.821e-02  1.834e-02  -0.993   0.3205  
## BP_SYSTOLIC_23                        -1.095e-02  1.774e-02  -0.617   0.5370  
## BP_DIASTOLIC_23                        4.567e-03  3.210e-02   0.142   0.8869  
## PMRC_LAB_GLU                           2.466e-02  1.421e-02   1.735   0.0827 .
## PMRC_LAB_GH                            1.311e+00  5.469e-01   2.396   0.0166 *
## ANT_MEAS_WAIST_CM                     -5.217e-02  4.020e-02  -1.298   0.1943  
## D_0__Archaea.D_1__Euryarchaeota        4.495e+01  3.119e+01   1.441   0.1495  
## D_0__Bacteria.D_1__Actinobacteria     -6.181e+01  2.651e+01  -2.331   0.0197 *
## D_0__Bacteria.D_1__Bacteroidetes      -1.716e+01  1.488e+01  -1.153   0.2489  
## D_0__Bacteria.D_1__Cyanobacteria       8.583e+01  3.761e+02   0.228   0.8195  
## D_0__Bacteria.D_1__Epsilonbacteraeota  5.610e+02  3.457e+03   0.162   0.8711  
## D_0__Bacteria.D_1__Firmicutes         -1.918e+01  1.503e+01  -1.276   0.2018  
## D_0__Bacteria.D_1__Fusobacteria        3.572e+02  2.584e+02   1.382   0.1669  
## D_0__Bacteria.D_1__Lentisphaerae      -7.244e+04  5.748e+06  -0.013   0.9899  
## D_0__Bacteria.D_1__Proteobacteria     -2.566e+01  1.698e+01  -1.511   0.1307  
## D_0__Bacteria.D_1__Synergistetes       3.226e+01  2.247e+02   0.144   0.8858  
## D_0__Bacteria.D_1__Tenericutes        -8.927e+01  7.894e+01  -1.131   0.2581  
## D_0__Bacteria.D_1__Verrucomicrobia            NA         NA      NA       NA  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 167.07  on 120  degrees of freedom
## Residual deviance: 116.95  on 100  degrees of freedom
##   (167 observations deleted due to missingness)
## AIC: 158.95
## 
## Number of Fisher Scoring iterations: 16
#Male
# the code below checks the sum of all numeric cols and removes any cols that sum to zero
colsums_male <- colSums(Filter(is.numeric,merged.table_male))
zero_cols <- names(colsums_male[colsums_male==0 & !is.na(colsums_male)])
# re-define merged.tale without cols that sum to zero
merged.table_male <- merged.table_male %>% select(-one_of(zero_cols))

#Female
# the code below checks the sum of all numeric cols and removes any cols that sum to zero
colsums_female <- colSums(Filter(is.numeric,merged.table_female))
zero_cols <- names(colsums_female[colsums_female==0 & !is.na(colsums_female)])
# re-define merged.tale without cols that sum to zero
merged.table_female <- merged.table_female %>% select(-one_of(zero_cols))

#Correlation test

multi_assoc <- function(mdf,exp_vars, res_vars, p.zeros=.25,adj.zero=TRUE,method, inc.zeros=TRUE, run_ratio = TRUE){
  #Arguments:
  # mdf - dataframe where the explanitory and response variables are as columns and subjects are rows
  # exp_vars - a vector of numbers that indicate the explanitory variable cols in mdf 
  # res_vars - a vector of numbers that indicate the response variable cols in mdf
  # p.zeros - the max amount of zeros in a singe variable that will be tolerated (expressed as a percent)
  # this taxa has to be 25% present in all samples to run the analysis.
  # adj.zeros - add a small value to each datapoint (0.1% of the variable average) to allow for divide by zero
  # add small number, so it's close to 0 but has some values (if running correlation with 0, causes problems)
  # method - 'spearman', 'pearson'
  # spearman brings values high to low [ranking]; whereas pearson uses the actual values; spearman corrects/reduces variation but p value less significant.
  # inc.zeros - TRUE = include all zeros in exp_vars for analysis. FALSE = replace all zeros wtih NA
  # run_ration - TRUE = it will run correlations for every exp_var1:exp_var2 combination to the response variable. If not "TRUE", will only run correlations with exp_var1 vs res_var
  
  
  
  # modification of multi_assoc(method = 'spearman', ). Only divides and multiplys explanitory variables
  if (inc.zeros==FALSE){
    mdf[,exp_vars] <- apply(mdf[,exp_vars], 2, function(x) ifelse(x == 0, NA, x))
  }
  mdf$None <- c(rep(1,nrow(mdf)))
  exp_vars <- c(exp_vars,match('None', colnames(mdf)))
  d <- list()
  n <- 0
  t=1
  col_headers <- c("Explanitory_var1","Explanitory_var2","Response_var", "Estimate", "c.Pval", "Rsq", 'r.Pval')
  if(adj.zero == TRUE){ #check to see if adjustment was specified
    adj=1
  }else{
    adj=0
  }
  for (i in exp_vars[-length(exp_vars)]) { #for every exp variable. This excludes the "None" column added in line above
    if ((length(which(mdf[,i]==0|is.na(mdf[,i])==TRUE))<p.zeros*length(mdf[,i])) & (is.numeric(mdf[,i])==TRUE)){ # if the percent of zeros in exp var is less than the specified p.zero threshold, continue, else skip exp var
      if (run_ratio == TRUE){
        list2 <- exp_vars[-match(i, exp_vars)] #makes a list of all variables except for "i" variable to loop over (for divide only, see multiply below)
      } else {
        list2 <- 'None'
      }
      for (j in list2){
        if ((length(which(mdf[,j]==0|is.na(mdf[,j])==TRUE))<p.zeros*length(mdf[,j])) & (is.numeric(mdf[,j])==TRUE)){ #check to see if comparison exp var meets p.zero threshold
          for (x in res_vars){ #loops over every response variable
            #run tests
            z <- (mdf[,i]+adj*(0.001*mean(mdf[,i],na.rm = T)))/(mdf[,j]+adj*(0.001*mean(mdf[,j],na.rm = T)))
            z[is.infinite(z)] <- NA
            y <- mdf[,x]
            tmp <- cor.test(y, z, method = method)
            reg <- summary(lm(y~z))
            tmp_df <- data.frame(
              colnames(mdf[i]),
              colnames(mdf[j]),
              colnames(mdf[x]),
              as.numeric(tmp[4]), 
              as.numeric(tmp[3]),
              as.numeric(reg$r.squared),
              as.numeric(try(pf(reg$fstatistic[1],reg$fstatistic[2],reg$fstatistic[3], lower.tail = F),silent = T)),
              stringsAsFactors = FALSE)
            n <- n+1
            d[[n]] <- tmp_df
          }
        }
      }
    }
    if (t > (length(exp_vars)/100)){ # prints status as a percentage
      print(paste(match(i,exp_vars)/length(exp_vars)*100,"%"))
      t=1
    }else{
      t=t+1
    }
  }
  tmp_results <- do.call(rbind,d)
  colnames(tmp_results) <- col_headers
  tmp_results <- as_data_frame(tmp_results)
  tmp_results$c.fdr <- p.adjust(tmp_results$c.Pval)
  cp <- match("c.Pval", colnames(tmp_results))
  tmp_results <- tmp_results[,c(1:cp, ncol(tmp_results),(cp+1):(ncol(tmp_results)-1))]
  tmp_results$r.fdr <- p.adjust(tmp_results$r.Pval)
  multi_corr_tbl <- tmp_results[order(tmp_results$c.Pval, decreasing = F),]
  rownames(multi_corr_tbl) <- c(1:nrow(multi_corr_tbl))
  multi_corr_tbl$index <- c(1:nrow(multi_corr_tbl))
  if (run_ratio != TRUE){
    multi_corr_tbl <- multi_corr_tbl[,-2]
  }
  return(multi_corr_tbl)
}

#####################################
#####################################

plot_comprsn <- function (data_tbl,comp_tbl,row,color.by='All samples'){
  #Arguments:
  # data_tbl - dataframe where the explanitory and response variables are as columns and subjects are rows (same df used in multi_pred_cor())
  # comp_tbl - comparison table, this is the output of multi_pred_cor()
  # row - the row of the comp_tbl you want to plot (row 1 is the most significant correlation)
  # color.by - the col of data_table to use as input for aes(color =). Must specify the col with $.
  
  
  
  
  if (colnames(comp_tbl[2]) != "Explanitory_var2"){
    tops <- c(comp_tbl[[row,1]], "", comp_tbl[[row,2]])
    z=data_tbl[[tops[1]]]
    label <- tops[1]
  } else {
    tops <- c(comp_tbl[[row,1]], comp_tbl[[row,2]], comp_tbl[[row,3]])
    if (tops[2]=="None"){
      z=data_tbl[[tops[1]]]
      label <- tops[1]
    } else {
      z <- do.call('/',list(data_tbl[[tops[1]]],data_tbl[[tops[2]]]))
      z[is.infinite(z)] <- NA
      label <- paste(tops[1], tops[2], sep = paste("_##","/","##_"))
    }
  }
  y <- tops[3]
  data_tbl$zn <- z
  x <- 'zn'
  my.formula <- x~y
  
  if (color.by != "All samples"){
    color.by <- data_tbl[,color.by]
    colors <- scale_color_brewer(palette="Set1")
  } else {
    colors <- scale_color_manual(values = 'black')
  }
  
  plot <- data_tbl %>% ggplot(aes(x = data_tbl$zn, y = data_tbl[,y], color=color.by))+
    xlab(label)+
    ylab(tops[3])+
    geom_point()+
    colors+
    stat_cor(method = 'spearman', label.y.npc = .95)+
    geom_smooth(method=lm, se=F)
  
  return(plot)
}

#Scaterplot and heatmap ##BMI

#Try each phenotype of the disease: phe = c(6:12,14,15)
phe = c(5) #BMI
#phe = c(6) #TRIG
# phe = c(7) #HDL
# phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist

taxa = c(20:31) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.3846153846154 %"
## [1] "23.0769230769231 %"
## [1] "30.7692307692308 %"
## [1] "38.4615384615385 %"
## [1] "46.1538461538462 %"
## [1] "53.8461538461538 %"
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## [1] "76.9230769230769 %"
## [1] "84.6153846153846 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning: `as_data_frame()` is deprecated as of tibble 2.0.0.
## Please use `as_tibble()` instead.
## The signature and semantics have changed, see `?as_tibble`.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

taxa = c(20:31) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.3846153846154 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.0769230769231 %"
## [1] "30.7692307692308 %"
## [1] "38.4615384615385 %"
## [1] "46.1538461538462 %"
## [1] "53.8461538461538 %"
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## [1] "76.9230769230769 %"
## [1] "84.6153846153846 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 2 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 2 rows containing non-finite values (stat_smooth).
## Warning: Removed 2 rows containing missing values (geom_point).

##TRIG

phe = c(6) #TRIG
# phe = c(7) #HDL
# phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist

taxa = c(20:31) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.3846153846154 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.0769230769231 %"
## [1] "30.7692307692308 %"
## [1] "38.4615384615385 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "53.8461538461538 %"
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## [1] "76.9230769230769 %"
## [1] "84.6153846153846 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 73 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 73 rows containing non-finite values (stat_smooth).
## Warning: Removed 73 rows containing missing values (geom_point).

taxa = c(20:31) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.3846153846154 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.0769230769231 %"
## [1] "30.7692307692308 %"
## [1] "38.4615384615385 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "53.8461538461538 %"
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## [1] "76.9230769230769 %"
## [1] "84.6153846153846 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 88 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 88 rows containing non-finite values (stat_smooth).
## Warning: Removed 88 rows containing missing values (geom_point).

##HDL

phe = c(7) #HDL
# phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist

taxa = c(20:31) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.3846153846154 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.0769230769231 %"
## [1] "30.7692307692308 %"
## [1] "38.4615384615385 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "53.8461538461538 %"
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## [1] "76.9230769230769 %"
## [1] "84.6153846153846 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 74 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 74 rows containing non-finite values (stat_smooth).
## Warning: Removed 74 rows containing missing values (geom_point).

taxa = c(20:31) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.3846153846154 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.0769230769231 %"
## [1] "30.7692307692308 %"
## [1] "38.4615384615385 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "53.8461538461538 %"
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## [1] "76.9230769230769 %"
## [1] "84.6153846153846 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 90 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 90 rows containing non-finite values (stat_smooth).
## Warning: Removed 90 rows containing missing values (geom_point).

##Systolic

phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist

taxa = c(20:31) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.3846153846154 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.0769230769231 %"
## [1] "30.7692307692308 %"
## [1] "38.4615384615385 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "53.8461538461538 %"
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## [1] "76.9230769230769 %"
## [1] "84.6153846153846 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

taxa = c(20:31) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.3846153846154 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.0769230769231 %"
## [1] "30.7692307692308 %"
## [1] "38.4615384615385 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "53.8461538461538 %"
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## [1] "76.9230769230769 %"
## [1] "84.6153846153846 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

##Diastolic

phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist

taxa = c(20:31) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.3846153846154 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.0769230769231 %"
## [1] "30.7692307692308 %"
## [1] "38.4615384615385 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "53.8461538461538 %"
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## [1] "76.9230769230769 %"
## [1] "84.6153846153846 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

taxa = c(20:31) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.3846153846154 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.0769230769231 %"
## [1] "30.7692307692308 %"
## [1] "38.4615384615385 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "53.8461538461538 %"
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## [1] "76.9230769230769 %"
## [1] "84.6153846153846 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

##GLU

phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist

taxa = c(20:31) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.3846153846154 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.0769230769231 %"
## [1] "30.7692307692308 %"
## [1] "38.4615384615385 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "53.8461538461538 %"
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## [1] "76.9230769230769 %"
## [1] "84.6153846153846 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 74 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 74 rows containing non-finite values (stat_smooth).
## Warning: Removed 74 rows containing missing values (geom_point).

taxa = c(20:31) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.3846153846154 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.0769230769231 %"
## [1] "30.7692307692308 %"
## [1] "38.4615384615385 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "53.8461538461538 %"
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## [1] "76.9230769230769 %"
## [1] "84.6153846153846 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 90 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 90 rows containing non-finite values (stat_smooth).
## Warning: Removed 90 rows containing missing values (geom_point).

##GH

phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist

taxa = c(20:31) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.3846153846154 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.0769230769231 %"
## [1] "30.7692307692308 %"
## [1] "38.4615384615385 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "53.8461538461538 %"
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## [1] "76.9230769230769 %"
## [1] "84.6153846153846 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 74 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 74 rows containing non-finite values (stat_smooth).
## Warning: Removed 74 rows containing missing values (geom_point).

taxa = c(20:31) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.3846153846154 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.0769230769231 %"
## [1] "30.7692307692308 %"
## [1] "38.4615384615385 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "53.8461538461538 %"
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## [1] "76.9230769230769 %"
## [1] "84.6153846153846 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 90 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 90 rows containing non-finite values (stat_smooth).
## Warning: Removed 90 rows containing missing values (geom_point).

##AGE

phe = c(13) #AGE
# phe = c(14) #Waist

taxa = c(20:31) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.3846153846154 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.0769230769231 %"
## [1] "30.7692307692308 %"
## [1] "38.4615384615385 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "53.8461538461538 %"
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## [1] "76.9230769230769 %"
## [1] "84.6153846153846 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

taxa = c(20:31) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.3846153846154 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.0769230769231 %"
## [1] "30.7692307692308 %"
## [1] "38.4615384615385 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "53.8461538461538 %"
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## [1] "76.9230769230769 %"
## [1] "84.6153846153846 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

##Waist

phe = c(14) #Waist

taxa = c(20:31) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.3846153846154 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.0769230769231 %"
## [1] "30.7692307692308 %"
## [1] "38.4615384615385 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "53.8461538461538 %"
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## [1] "76.9230769230769 %"
## [1] "84.6153846153846 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

taxa = c(20:31) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.3846153846154 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.0769230769231 %"
## [1] "30.7692307692308 %"
## [1] "38.4615384615385 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "53.8461538461538 %"
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## [1] "76.9230769230769 %"
## [1] "84.6153846153846 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

#Heatmap_level2

#Male
# Visualizing the correlation in heatmap [30x30]; try with class x class- level 3
library(corrplot)
## corrplot 0.84 loaded
res = cor.mtest(merged.table_male[,c(5:11,13,14,20:31)], conf.level = 0.95, rm.na = T)
## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero
Correlation <- round(cor(merged.table_male[,c(5:11,13,14,20:31)],method = "spearman", use="complete.obs"), 2)
## Warning in cor(merged.table_male[, c(5:11, 13, 14, 20:31)], method =
## "spearman", : the standard deviation is zero
corrplot(Correlation, method = "ellipse", tl.col = "black", type = 'upper', tl.cex = 0.4, cl.cex = 0.4, p.mat = res$p, insig = "blank", sig.level = 0.05) #heatmap; blue=neg corr; red=pos corr

#Female
# Visualizing the correlation in heatmap [30x30]; try with class x class- level 3
library(corrplot)
res = cor.mtest(merged.table_female[,c(5:11,13,14,20:31)], conf.level = 0.95, rm.na = T)
Correlation <- round(cor(merged.table_female[,c(5:11,13,14,20:31)],method = "spearman", use="complete.obs"), 2)
corrplot(Correlation, method = "ellipse", tl.col = "black", type = 'upper', tl.cex = 0.4, cl.cex = 0.4, p.mat = res$p, insig = "blank", sig.level = 0.05) #heatmap; blue=neg corr; red=pos corr

#Read dataframes_level3_class

#ASVs <- read_qza("microbiome_data/filtered/table_filt.qza") #Gives me an error so I commented out.
taxa_table <- read.csv("level-3_class_taxtable_clean.csv", header=T)
taxa_table = taxa_table[,1:21] #all rows, from columns 1 to 21
taxa_ra <- sweep(taxa_table[,2:ncol(taxa_table)],1,rowSums(taxa_table[,2:ncol(taxa_table)]),"/") #relative abundance - normalization of sample reads
taxa_ra$index = taxa_table$index
merged.table_class <- merge(MetS_feature, taxa_ra, by.x="16S_ID", by.y="index")

merged.table_male <- merged.table_class %>%
  filter(GENDER == "[1] Male")
merged.table_female <- merged.table_class %>%
  filter(GENDER == "[2] Female")

#Regression
MetS_feature$MetS <- ifelse((MetS_feature$MetS.binary == 1) | (MetS_feature$gh.binary ==1), 1, 0)
reg_data_class <- merged.table_class %>% select(MetS,AGE_CONSENT, ANT_BMI, PMRC_LAB_TRIG, PMRC_LAB_HDLCHOL, BP_SYSTOLIC_23, BP_DIASTOLIC_23, PMRC_LAB_GLU, PMRC_LAB_GH, ANT_MEAS_WAIST_CM, starts_with("D_0__"))
lmod <- glm(MetS ~ ., family = "binomial", data = reg_data_class)
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
summary(lmod)
## 
## Call:
## glm(formula = MetS ~ ., family = "binomial", data = reg_data_class)
## 
## Deviance Residuals: 
##      Min        1Q    Median        3Q       Max  
## -2.32446  -0.71129  -0.02904   0.59642   2.04943  
## 
## Coefficients: (1 not defined because of singularities)
##                                                              Estimate
## (Intercept)                                                 2.254e+01
## AGE_CONSENT                                                -8.165e-02
## ANT_BMI                                                     2.063e-02
## PMRC_LAB_TRIG                                               5.487e-03
## PMRC_LAB_HDLCHOL                                           -2.757e-02
## BP_SYSTOLIC_23                                              1.766e-02
## BP_DIASTOLIC_23                                            -2.825e-02
## PMRC_LAB_GLU                                                3.255e-02
## PMRC_LAB_GH                                                 1.203e+00
## ANT_MEAS_WAIST_CM                                          -6.906e-02
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria        2.969e+01
## D_0__Archaea.D_1__Euryarchaeota.D_2__Thermoplasmata         1.035e+03
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria      -9.173e+01
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia       2.499e+01
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia          -1.892e+01
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria       1.254e+03
## D_0__Bacteria.D_1__Epsilonbacteraeota.D_2__Campylobacteria -2.058e+02
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli                  1.228e+00
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia              -2.337e+01
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia        -3.235e+01
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes            8.779e+00
## D_0__Bacteria.D_1__Firmicutes.__                            9.883e+03
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia          4.699e+02
## D_0__Bacteria.D_1__Lentisphaerae.D_2__Lentisphaeria        -7.689e+04
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria -8.053e+02
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria -1.018e+02
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria -3.090e+01
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia           4.632e+01
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes             -3.169e+02
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae           NA
##                                                            Std. Error z value
## (Intercept)                                                 2.033e+01   1.109
## AGE_CONSENT                                                 3.040e-02  -2.686
## ANT_BMI                                                     1.024e-01   0.201
## PMRC_LAB_TRIG                                               3.919e-03   1.400
## PMRC_LAB_HDLCHOL                                            2.186e-02  -1.261
## BP_SYSTOLIC_23                                              2.361e-02   0.748
## BP_DIASTOLIC_23                                             3.844e-02  -0.735
## PMRC_LAB_GLU                                                1.687e-02   1.930
## PMRC_LAB_GH                                                 7.625e-01   1.577
## ANT_MEAS_WAIST_CM                                           5.163e-02  -1.338
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria        3.970e+01   0.748
## D_0__Archaea.D_1__Euryarchaeota.D_2__Thermoplasmata         4.566e+03   0.227
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria       3.618e+01  -2.535
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia       1.018e+02   0.246
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia           1.899e+01  -0.997
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria       7.061e+02   1.776
## D_0__Bacteria.D_1__Epsilonbacteraeota.D_2__Campylobacteria  5.597e+03  -0.037
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli                  2.678e+01   0.046
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia               1.910e+01  -1.223
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia         2.791e+01  -1.159
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes            2.607e+01   0.337
## D_0__Bacteria.D_1__Firmicutes.__                            4.794e+03   2.061
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia          2.772e+02   1.695
## D_0__Bacteria.D_1__Lentisphaerae.D_2__Lentisphaeria         8.207e+06  -0.009
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria  4.681e+02  -1.720
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria  1.192e+02  -0.854
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria  2.053e+01  -1.505
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia           6.630e+02   0.070
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes              3.113e+02  -1.018
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae           NA      NA
##                                                            Pr(>|z|)   
## (Intercept)                                                 0.26746   
## AGE_CONSENT                                                 0.00724 **
## ANT_BMI                                                     0.84038   
## PMRC_LAB_TRIG                                               0.16148   
## PMRC_LAB_HDLCHOL                                            0.20729   
## BP_SYSTOLIC_23                                              0.45467   
## BP_DIASTOLIC_23                                             0.46238   
## PMRC_LAB_GLU                                                0.05362 . 
## PMRC_LAB_GH                                                 0.11469   
## ANT_MEAS_WAIST_CM                                           0.18100   
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria        0.45453   
## D_0__Archaea.D_1__Euryarchaeota.D_2__Thermoplasmata         0.82062   
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria       0.01124 * 
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia       0.80601   
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia           0.31897   
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria       0.07566 . 
## D_0__Bacteria.D_1__Epsilonbacteraeota.D_2__Campylobacteria  0.97067   
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli                  0.96343   
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia               0.22126   
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia         0.24649   
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes            0.73634   
## D_0__Bacteria.D_1__Firmicutes.__                            0.03927 * 
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia          0.09004 . 
## D_0__Bacteria.D_1__Lentisphaerae.D_2__Lentisphaeria         0.99252   
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria  0.08535 . 
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria  0.39298   
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria  0.13227   
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia           0.94430   
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes              0.30870   
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae         NA   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 167.072  on 120  degrees of freedom
## Residual deviance:  94.889  on  92  degrees of freedom
##   (167 observations deleted due to missingness)
## AIC: 152.89
## 
## Number of Fisher Scoring iterations: 17
#Male
# the code below checks the sum of all numeric cols and removes any cols that sum to zero
colsums_male <- colSums(Filter(is.numeric,merged.table_male))
zero_cols <- names(colsums_male[colsums_male==0 & !is.na(colsums_male)])
# re-define merged.tale without cols that sum to zero
merged.table_male <- merged.table_male %>% select(-one_of(zero_cols))

#Female
# the code below checks the sum of all numeric cols and removes any cols that sum to zero
colsums_female <- colSums(Filter(is.numeric,merged.table_female))
zero_cols <- names(colsums_female[colsums_female==0 & !is.na(colsums_female)])
# re-define merged.tale without cols that sum to zero
merged.table_female <- merged.table_female %>% select(-one_of(zero_cols))

#Correlation test

multi_assoc <- function(mdf,exp_vars, res_vars, p.zeros=.25,adj.zero=TRUE,method, inc.zeros=TRUE, run_ratio = TRUE){
  #Arguments:
  # mdf - dataframe where the explanitory and response variables are as columns and subjects are rows
  # exp_vars - a vector of numbers that indicate the explanitory variable cols in mdf 
  # res_vars - a vector of numbers that indicate the response variable cols in mdf
  # p.zeros - the max amount of zeros in a singe variable that will be tolerated (expressed as a percent)
  # this taxa has to be 25% present in all samples to run the analysis.
  # adj.zeros - add a small value to each datapoint (0.1% of the variable average) to allow for divide by zero
  # add small number, so it's close to 0 but has some values (if running correlation with 0, causes problems)
  # method - 'spearman', 'pearson'
  # spearman brings values high to low [ranking]; whereas pearson uses the actual values; spearman corrects/reduces variation but p value less significant.
  # inc.zeros - TRUE = include all zeros in exp_vars for analysis. FALSE = replace all zeros wtih NA
  # run_ration - TRUE = it will run correlations for every exp_var1:exp_var2 combination to the response variable. If not "TRUE", will only run correlations with exp_var1 vs res_var
  
  
  
  # modification of multi_assoc(method = 'spearman', ). Only divides and multiplys explanitory variables
  if (inc.zeros==FALSE){
    mdf[,exp_vars] <- apply(mdf[,exp_vars], 2, function(x) ifelse(x == 0, NA, x))
  }
  mdf$None <- c(rep(1,nrow(mdf)))
  exp_vars <- c(exp_vars,match('None', colnames(mdf)))
  d <- list()
  n <- 0
  t=1
  col_headers <- c("Explanitory_var1","Explanitory_var2","Response_var", "Estimate", "c.Pval", "Rsq", 'r.Pval')
  if(adj.zero == TRUE){ #check to see if adjustment was specified
    adj=1
  }else{
    adj=0
  }
  for (i in exp_vars[-length(exp_vars)]) { #for every exp variable. This excludes the "None" column added in line above
    if ((length(which(mdf[,i]==0|is.na(mdf[,i])==TRUE))<p.zeros*length(mdf[,i])) & (is.numeric(mdf[,i])==TRUE)){ # if the percent of zeros in exp var is less than the specified p.zero threshold, continue, else skip exp var
      if (run_ratio == TRUE){
        list2 <- exp_vars[-match(i, exp_vars)] #makes a list of all variables except for "i" variable to loop over (for divide only, see multiply below)
      } else {
        list2 <- 'None'
      }
      for (j in list2){
        if ((length(which(mdf[,j]==0|is.na(mdf[,j])==TRUE))<p.zeros*length(mdf[,j])) & (is.numeric(mdf[,j])==TRUE)){ #check to see if comparison exp var meets p.zero threshold
          for (x in res_vars){ #loops over every response variable
            #run tests
            z <- (mdf[,i]+adj*(0.001*mean(mdf[,i],na.rm = T)))/(mdf[,j]+adj*(0.001*mean(mdf[,j],na.rm = T)))
            z[is.infinite(z)] <- NA
            y <- mdf[,x]
            tmp <- cor.test(y, z, method = method)
            reg <- summary(lm(y~z))
            tmp_df <- data.frame(
              colnames(mdf[i]),
              colnames(mdf[j]),
              colnames(mdf[x]),
              as.numeric(tmp[4]), 
              as.numeric(tmp[3]),
              as.numeric(reg$r.squared),
              as.numeric(try(pf(reg$fstatistic[1],reg$fstatistic[2],reg$fstatistic[3], lower.tail = F),silent = T)),
              stringsAsFactors = FALSE)
            n <- n+1
            d[[n]] <- tmp_df
          }
        }
      }
    }
    if (t > (length(exp_vars)/100)){ # prints status as a percentage
      print(paste(match(i,exp_vars)/length(exp_vars)*100,"%"))
      t=1
    }else{
      t=t+1
    }
  }
  tmp_results <- do.call(rbind,d)
  colnames(tmp_results) <- col_headers
  tmp_results <- as_data_frame(tmp_results)
  tmp_results$c.fdr <- p.adjust(tmp_results$c.Pval)
  cp <- match("c.Pval", colnames(tmp_results))
  tmp_results <- tmp_results[,c(1:cp, ncol(tmp_results),(cp+1):(ncol(tmp_results)-1))]
  tmp_results$r.fdr <- p.adjust(tmp_results$r.Pval)
  multi_corr_tbl <- tmp_results[order(tmp_results$c.Pval, decreasing = F),]
  rownames(multi_corr_tbl) <- c(1:nrow(multi_corr_tbl))
  multi_corr_tbl$index <- c(1:nrow(multi_corr_tbl))
  if (run_ratio != TRUE){
    multi_corr_tbl <- multi_corr_tbl[,-2]
  }
  return(multi_corr_tbl)
}

#####################################
#####################################

plot_comprsn <- function (data_tbl,comp_tbl,row,color.by='All samples'){
  #Arguments:
  # data_tbl - dataframe where the explanitory and response variables are as columns and subjects are rows (same df used in multi_pred_cor())
  # comp_tbl - comparison table, this is the output of multi_pred_cor()
  # row - the row of the comp_tbl you want to plot (row 1 is the most significant correlation)
  # color.by - the col of data_table to use as input for aes(color =). Must specify the col with $.
  
  
  
  
  if (colnames(comp_tbl[2]) != "Explanitory_var2"){
    tops <- c(comp_tbl[[row,1]], "", comp_tbl[[row,2]])
    z=data_tbl[[tops[1]]]
    label <- tops[1]
  } else {
    tops <- c(comp_tbl[[row,1]], comp_tbl[[row,2]], comp_tbl[[row,3]])
    if (tops[2]=="None"){
      z=data_tbl[[tops[1]]]
      label <- tops[1]
    } else {
      z <- do.call('/',list(data_tbl[[tops[1]]],data_tbl[[tops[2]]]))
      z[is.infinite(z)] <- NA
      label <- paste(tops[1], tops[2], sep = paste("_##","/","##_"))
    }
  }
  y <- tops[3]
  data_tbl$zn <- z
  x <- 'zn'
  my.formula <- x~y
  
  if (color.by != "All samples"){
    color.by <- data_tbl[,color.by]
    colors <- scale_color_brewer(palette="Set1")
  } else {
    colors <- scale_color_manual(values = 'black')
  }
  
  plot <- data_tbl %>% ggplot(aes(x = data_tbl$zn, y = data_tbl[,y], color=color.by))+
    xlab(label)+
    ylab(tops[3])+
    geom_point()+
    colors+
    stat_cor(method = 'spearman', label.y.npc = .95)+
    geom_smooth(method=lm, se=F)
  
  return(plot)
}

#Scaterplot and heatmap ##BMI

#Try each phenotype of the disease: phe = c(6:12,14,15)
phe = c(5) #BMI
#phe = c(6) #TRIG
# phe = c(7) #HDL
# phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist

taxa = c(20:38) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "5 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15 %"
## [1] "20 %"
## [1] "25 %"
## [1] "30 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "35 %"
## [1] "40 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "45 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "50 %"
## [1] "55 %"
## [1] "60 %"
## [1] "65 %"
## [1] "70 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80 %"
## [1] "85 %"
## [1] "90 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "95 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

taxa = c(20:39) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "4.76190476190476 %"
## [1] "9.52380952380952 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "14.2857142857143 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.047619047619 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.8095238095238 %"
## [1] "28.5714285714286 %"
## [1] "33.3333333333333 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "38.0952380952381 %"
## [1] "42.8571428571429 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.6190476190476 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "52.3809523809524 %"
## [1] "57.1428571428571 %"
## [1] "61.9047619047619 %"
## [1] "66.6666666666667 %"
## [1] "71.4285714285714 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.1904761904762 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80.9523809523809 %"
## [1] "85.7142857142857 %"
## [1] "90.4761904761905 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "95.2380952380952 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 2 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 2 rows containing non-finite values (stat_smooth).
## Warning: Removed 2 rows containing missing values (geom_point).

##TRIG

phe = c(6) #TRIG
# phe = c(7) #HDL
# phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist

taxa = c(20:38) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "5 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "20 %"
## [1] "25 %"
## [1] "30 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "35 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "40 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "45 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "50 %"
## [1] "55 %"
## [1] "60 %"
## [1] "65 %"
## [1] "70 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80 %"
## [1] "85 %"
## [1] "90 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "95 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 73 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 73 rows containing non-finite values (stat_smooth).
## Warning: Removed 73 rows containing missing values (geom_point).

taxa = c(20:39) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "4.76190476190476 %"
## [1] "9.52380952380952 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "14.2857142857143 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.047619047619 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.8095238095238 %"
## [1] "28.5714285714286 %"
## [1] "33.3333333333333 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "38.0952380952381 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.8571428571429 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.6190476190476 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "52.3809523809524 %"
## [1] "57.1428571428571 %"
## [1] "61.9047619047619 %"
## [1] "66.6666666666667 %"
## [1] "71.4285714285714 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.1904761904762 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80.9523809523809 %"
## [1] "85.7142857142857 %"
## [1] "90.4761904761905 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "95.2380952380952 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 88 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 88 rows containing non-finite values (stat_smooth).
## Warning: Removed 88 rows containing missing values (geom_point).

##HDL

phe = c(7) #HDL
# phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist

taxa = c(20:38) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "5 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "20 %"
## [1] "25 %"
## [1] "30 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "35 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "40 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "45 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "50 %"
## [1] "55 %"
## [1] "60 %"
## [1] "65 %"
## [1] "70 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80 %"
## [1] "85 %"
## [1] "90 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "95 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 74 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 74 rows containing non-finite values (stat_smooth).
## Warning: Removed 74 rows containing missing values (geom_point).

taxa = c(20:39) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "4.76190476190476 %"
## [1] "9.52380952380952 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "14.2857142857143 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.047619047619 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.8095238095238 %"
## [1] "28.5714285714286 %"
## [1] "33.3333333333333 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "38.0952380952381 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.8571428571429 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.6190476190476 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "52.3809523809524 %"
## [1] "57.1428571428571 %"
## [1] "61.9047619047619 %"
## [1] "66.6666666666667 %"
## [1] "71.4285714285714 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.1904761904762 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80.9523809523809 %"
## [1] "85.7142857142857 %"
## [1] "90.4761904761905 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "95.2380952380952 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 90 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 90 rows containing non-finite values (stat_smooth).
## Warning: Removed 90 rows containing missing values (geom_point).

##Systolic

phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist

taxa = c(20:38) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "5 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "20 %"
## [1] "25 %"
## [1] "30 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "35 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "40 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "45 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "50 %"
## [1] "55 %"
## [1] "60 %"
## [1] "65 %"
## [1] "70 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80 %"
## [1] "85 %"
## [1] "90 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "95 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

taxa = c(20:39) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "4.76190476190476 %"
## [1] "9.52380952380952 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "14.2857142857143 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.047619047619 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.8095238095238 %"
## [1] "28.5714285714286 %"
## [1] "33.3333333333333 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "38.0952380952381 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.8571428571429 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.6190476190476 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "52.3809523809524 %"
## [1] "57.1428571428571 %"
## [1] "61.9047619047619 %"
## [1] "66.6666666666667 %"
## [1] "71.4285714285714 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.1904761904762 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80.9523809523809 %"
## [1] "85.7142857142857 %"
## [1] "90.4761904761905 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "95.2380952380952 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

##Diastolic

phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist

taxa = c(20:38) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "5 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "20 %"
## [1] "25 %"
## [1] "30 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "35 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "40 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "45 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "50 %"
## [1] "55 %"
## [1] "60 %"
## [1] "65 %"
## [1] "70 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80 %"
## [1] "85 %"
## [1] "90 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "95 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

taxa = c(20:39) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "4.76190476190476 %"
## [1] "9.52380952380952 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "14.2857142857143 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.047619047619 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.8095238095238 %"
## [1] "28.5714285714286 %"
## [1] "33.3333333333333 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "38.0952380952381 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.8571428571429 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.6190476190476 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "52.3809523809524 %"
## [1] "57.1428571428571 %"
## [1] "61.9047619047619 %"
## [1] "66.6666666666667 %"
## [1] "71.4285714285714 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.1904761904762 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80.9523809523809 %"
## [1] "85.7142857142857 %"
## [1] "90.4761904761905 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "95.2380952380952 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

##GLU

phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist

taxa = c(20:38) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "5 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "20 %"
## [1] "25 %"
## [1] "30 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "35 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "40 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "45 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "50 %"
## [1] "55 %"
## [1] "60 %"
## [1] "65 %"
## [1] "70 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80 %"
## [1] "85 %"
## [1] "90 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "95 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 74 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 74 rows containing non-finite values (stat_smooth).
## Warning: Removed 74 rows containing missing values (geom_point).

taxa = c(20:39) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "4.76190476190476 %"
## [1] "9.52380952380952 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "14.2857142857143 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.047619047619 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.8095238095238 %"
## [1] "28.5714285714286 %"
## [1] "33.3333333333333 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "38.0952380952381 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.8571428571429 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.6190476190476 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "52.3809523809524 %"
## [1] "57.1428571428571 %"
## [1] "61.9047619047619 %"
## [1] "66.6666666666667 %"
## [1] "71.4285714285714 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.1904761904762 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80.9523809523809 %"
## [1] "85.7142857142857 %"
## [1] "90.4761904761905 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "95.2380952380952 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 90 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 90 rows containing non-finite values (stat_smooth).
## Warning: Removed 90 rows containing missing values (geom_point).

##GH

phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist

taxa = c(20:38) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "5 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "20 %"
## [1] "25 %"
## [1] "30 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "35 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "40 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "45 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "50 %"
## [1] "55 %"
## [1] "60 %"
## [1] "65 %"
## [1] "70 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80 %"
## [1] "85 %"
## [1] "90 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "95 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 74 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 74 rows containing non-finite values (stat_smooth).
## Warning: Removed 74 rows containing missing values (geom_point).

taxa = c(20:39) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "4.76190476190476 %"
## [1] "9.52380952380952 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "14.2857142857143 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.047619047619 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.8095238095238 %"
## [1] "28.5714285714286 %"
## [1] "33.3333333333333 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "38.0952380952381 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.8571428571429 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.6190476190476 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "52.3809523809524 %"
## [1] "57.1428571428571 %"
## [1] "61.9047619047619 %"
## [1] "66.6666666666667 %"
## [1] "71.4285714285714 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.1904761904762 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80.9523809523809 %"
## [1] "85.7142857142857 %"
## [1] "90.4761904761905 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "95.2380952380952 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 90 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 90 rows containing non-finite values (stat_smooth).
## Warning: Removed 90 rows containing missing values (geom_point).

##AGE

phe = c(13) #AGE
# phe = c(14) #Waist

taxa = c(20:38) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "5 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "20 %"
## [1] "25 %"
## [1] "30 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "35 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "40 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "45 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "50 %"
## [1] "55 %"
## [1] "60 %"
## [1] "65 %"
## [1] "70 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80 %"
## [1] "85 %"
## [1] "90 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "95 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

taxa = c(20:39) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "4.76190476190476 %"
## [1] "9.52380952380952 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "14.2857142857143 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.047619047619 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.8095238095238 %"
## [1] "28.5714285714286 %"
## [1] "33.3333333333333 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "38.0952380952381 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.8571428571429 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.6190476190476 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "52.3809523809524 %"
## [1] "57.1428571428571 %"
## [1] "61.9047619047619 %"
## [1] "66.6666666666667 %"
## [1] "71.4285714285714 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.1904761904762 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80.9523809523809 %"
## [1] "85.7142857142857 %"
## [1] "90.4761904761905 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "95.2380952380952 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

##Waist

phe = c(14) #Waist

taxa = c(20:38) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "5 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "20 %"
## [1] "25 %"
## [1] "30 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "35 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "40 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "45 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "50 %"
## [1] "55 %"
## [1] "60 %"
## [1] "65 %"
## [1] "70 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80 %"
## [1] "85 %"
## [1] "90 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "95 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

taxa = c(20:39) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "4.76190476190476 %"
## [1] "9.52380952380952 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "14.2857142857143 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.047619047619 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.8095238095238 %"
## [1] "28.5714285714286 %"
## [1] "33.3333333333333 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "38.0952380952381 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.8571428571429 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.6190476190476 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "52.3809523809524 %"
## [1] "57.1428571428571 %"
## [1] "61.9047619047619 %"
## [1] "66.6666666666667 %"
## [1] "71.4285714285714 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.1904761904762 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80.9523809523809 %"
## [1] "85.7142857142857 %"
## [1] "90.4761904761905 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "95.2380952380952 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

#Heatmap_level3

#Male
library(corrplot)
res = cor.mtest(merged.table_male[,c(5:11,13,14,20:38)], conf.level = 0.95, rm.na = T)
## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero
Correlation <- round(cor(merged.table_male[,c(5:11,13,14,20:38)],method = "spearman", use="complete.obs"), 2)
## Warning in cor(merged.table_male[, c(5:11, 13, 14, 20:38)], method =
## "spearman", : the standard deviation is zero
corrplot(Correlation, method = "ellipse", tl.col = "black", type = 'upper', tl.cex = 0.4, cl.cex = 0.4, p.mat = res$p, insig = "blank", sig.level = 0.05) #heatmap; blue=neg corr; red=pos corr

#Female
library(corrplot)
res = cor.mtest(merged.table_female[,c(5:11,13,14,20:39)], conf.level = 0.95, rm.na = T)
Correlation <- round(cor(merged.table_female[,c(5:11,13,14,20:30)],method = "spearman", use="complete.obs"), 2)
corrplot(Correlation, method = "ellipse", tl.col = "black", type = 'upper', tl.cex = 0.4, cl.cex = 0.4, p.mat = res$p, insig = "blank", sig.level = 0.05) #heatmap; blue=neg corr; red=pos corr

#Read dataframes_level4_order

#ASVs <- read_qza("microbiome_data/filtered/table_filt.qza") #Gives me an error so I commented out.
taxa_table <- read.csv("level-4_order_taxtable_clean.csv", header=T) # csv obtained from /Users/giovanna/OneDrive - UW-Madison/Rotations/3 Denu-Rey/SHOW data/microbiome_data/taxa/taxa_barplot.qza
taxa_table = taxa_table[,1:35] #all rows, from columns 1 to 35
taxa_ra <- sweep(taxa_table[,2:ncol(taxa_table)],1,rowSums(taxa_table[,2:ncol(taxa_table)]),"/") #relative abundance - normalization of sample reads
taxa_ra$index = taxa_table$index
merged.table_order <- merge(MetS_feature, taxa_ra, by.x="16S_ID", by.y="index")

merged.table_male <- merged.table_order %>%
  filter(GENDER == "[1] Male")
merged.table_female <- merged.table_order %>%
  filter(GENDER == "[2] Female")

#Regression
MetS_feature$MetS <- ifelse((MetS_feature$MetS.binary == 1) | (MetS_feature$gh.binary ==1), 1, 0)
reg_data_order <- merged.table_order %>% select(MetS,AGE_CONSENT, ANT_BMI, PMRC_LAB_TRIG, PMRC_LAB_HDLCHOL, BP_SYSTOLIC_23, BP_DIASTOLIC_23, PMRC_LAB_GLU, PMRC_LAB_GH, ANT_MEAS_WAIST_CM, starts_with("D_0__"))
lmod <- glm(MetS ~ ., family = "binomial", data = reg_data_order)
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
summary(lmod)
## 
## Call:
## glm(formula = MetS ~ ., family = "binomial", data = reg_data_order)
## 
## Deviance Residuals: 
##      Min        1Q    Median        3Q       Max  
## -2.28435  -0.48984  -0.00012   0.28948   2.18997  
## 
## Coefficients: (4 not defined because of singularities)
##                                                                                         Estimate
## (Intercept)                                                                            3.993e+01
## AGE_CONSENT                                                                           -1.143e-01
## ANT_BMI                                                                               -6.735e-02
## PMRC_LAB_TRIG                                                                          6.895e-03
## PMRC_LAB_HDLCHOL                                                                      -3.721e-02
## BP_SYSTOLIC_23                                                                         3.423e-02
## BP_DIASTOLIC_23                                                                       -5.865e-02
## PMRC_LAB_GLU                                                                           4.642e-02
## PMRC_LAB_GH                                                                            1.510e+00
## ANT_MEAS_WAIST_CM                                                                     -5.964e-02
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria.D_3__Methanobacteriales           6.198e+01
## D_0__Archaea.D_1__Euryarchaeota.D_2__Thermoplasmata.D_3__Methanomassiliicoccales      -6.287e+03
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales            -8.854e+01
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Bifidobacteriales          -1.181e+02
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Corynebacteriales           4.103e+06
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Micrococcales              -5.475e+04
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales            5.004e+01
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales                  -3.461e+01
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Flavobacteriales               -5.806e+04
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Sphingobacteriales                     NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales         2.723e+03
## D_0__Bacteria.D_1__Epsilonbacteraeota.D_2__Campylobacteria.D_3__Campylobacterales     -1.457e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales                            -1.845e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales                        5.572e+00
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales                      -4.160e+01
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.__                                      -1.798e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales           -3.740e+01
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales                  3.574e+01
## D_0__Bacteria.D_1__Firmicutes.__.__                                                    1.296e+04
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia.D_3__Fusobacteriales                7.815e+02
## D_0__Bacteria.D_1__Lentisphaerae.D_2__Lentisphaeria.D_3__Victivallales                -8.763e+04
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales      -1.599e+03
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.__                                 NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales    -2.499e+02
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Aeromonadales         -1.851e+03
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales -1.037e+02
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales     -5.234e+01
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pasteurellales        -9.168e+01
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pseudomonadales       -1.618e+03
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales                   1.463e+00
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales                   2.061e+03
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39                   -3.565e+02
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Opitutales                      NA
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Verrucomicrobiales              NA
##                                                                                       Std. Error
## (Intercept)                                                                            2.731e+01
## AGE_CONSENT                                                                            4.070e-02
## ANT_BMI                                                                                1.277e-01
## PMRC_LAB_TRIG                                                                          4.737e-03
## PMRC_LAB_HDLCHOL                                                                       2.792e-02
## BP_SYSTOLIC_23                                                                         3.275e-02
## BP_DIASTOLIC_23                                                                        6.103e-02
## PMRC_LAB_GLU                                                                           2.347e-02
## PMRC_LAB_GH                                                                            1.152e+00
## ANT_MEAS_WAIST_CM                                                                      6.227e-02
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria.D_3__Methanobacteriales           6.465e+01
## D_0__Archaea.D_1__Euryarchaeota.D_2__Thermoplasmata.D_3__Methanomassiliicoccales       1.235e+04
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales             1.716e+03
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Bifidobacteriales           3.995e+01
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Corynebacteriales           5.331e+08
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Micrococcales               3.435e+04
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales            1.542e+02
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales                   2.559e+01
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Flavobacteriales                7.419e+06
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Sphingobacteriales                     NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales         1.458e+03
## D_0__Bacteria.D_1__Epsilonbacteraeota.D_2__Campylobacteria.D_3__Campylobacterales      8.122e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales                             7.094e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales                        3.344e+01
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales                       2.572e+01
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.__                                       1.226e+04
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales            3.376e+01
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales                  3.349e+01
## D_0__Bacteria.D_1__Firmicutes.__.__                                                    6.480e+03
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia.D_3__Fusobacteriales                3.435e+02
## D_0__Bacteria.D_1__Lentisphaerae.D_2__Lentisphaeria.D_3__Victivallales                 1.877e+07
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales       7.612e+02
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.__                                 NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales     1.766e+02
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Aeromonadales          7.148e+02
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales  7.250e+01
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales      2.703e+01
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pasteurellales         4.859e+02
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pseudomonadales        1.414e+04
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales                   9.044e+02
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales                   1.907e+03
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39                    2.954e+02
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Opitutales                      NA
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Verrucomicrobiales              NA
##                                                                                       z value
## (Intercept)                                                                             1.462
## AGE_CONSENT                                                                            -2.807
## ANT_BMI                                                                                -0.527
## PMRC_LAB_TRIG                                                                           1.456
## PMRC_LAB_HDLCHOL                                                                       -1.333
## BP_SYSTOLIC_23                                                                          1.045
## BP_DIASTOLIC_23                                                                        -0.961
## PMRC_LAB_GLU                                                                            1.978
## PMRC_LAB_GH                                                                             1.311
## ANT_MEAS_WAIST_CM                                                                      -0.958
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria.D_3__Methanobacteriales            0.959
## D_0__Archaea.D_1__Euryarchaeota.D_2__Thermoplasmata.D_3__Methanomassiliicoccales       -0.509
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales             -0.052
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Bifidobacteriales           -2.957
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Corynebacteriales            0.008
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Micrococcales               -1.594
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales             0.324
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales                   -1.352
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Flavobacteriales                -0.008
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Sphingobacteriales                  NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales          1.868
## D_0__Bacteria.D_1__Epsilonbacteraeota.D_2__Campylobacteria.D_3__Campylobacterales      -0.179
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales                             -0.260
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales                         0.167
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales                       -1.618
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.__                                       -0.147
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales            -1.108
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales                   1.067
## D_0__Bacteria.D_1__Firmicutes.__.__                                                     2.001
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia.D_3__Fusobacteriales                 2.276
## D_0__Bacteria.D_1__Lentisphaerae.D_2__Lentisphaeria.D_3__Victivallales                 -0.005
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales       -2.100
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.__                              NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales     -1.415
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Aeromonadales          -2.589
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales  -1.430
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales      -1.936
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pasteurellales         -0.189
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pseudomonadales        -0.114
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales                    0.002
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales                    1.081
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39                    -1.207
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Opitutales                   NA
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Verrucomicrobiales           NA
##                                                                                       Pr(>|z|)
## (Intercept)                                                                            0.14362
## AGE_CONSENT                                                                            0.00500
## ANT_BMI                                                                                0.59799
## PMRC_LAB_TRIG                                                                          0.14552
## PMRC_LAB_HDLCHOL                                                                       0.18264
## BP_SYSTOLIC_23                                                                         0.29591
## BP_DIASTOLIC_23                                                                        0.33652
## PMRC_LAB_GLU                                                                           0.04791
## PMRC_LAB_GH                                                                            0.18989
## ANT_MEAS_WAIST_CM                                                                      0.33819
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria.D_3__Methanobacteriales           0.33769
## D_0__Archaea.D_1__Euryarchaeota.D_2__Thermoplasmata.D_3__Methanomassiliicoccales       0.61064
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales             0.95886
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Bifidobacteriales           0.00311
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Corynebacteriales           0.99386
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Micrococcales               0.11096
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales            0.74562
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales                   0.17622
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Flavobacteriales                0.99376
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Sphingobacteriales                   NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales         0.06170
## D_0__Bacteria.D_1__Epsilonbacteraeota.D_2__Campylobacteria.D_3__Campylobacterales      0.85760
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales                             0.79482
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales                        0.86767
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales                       0.10574
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.__                                       0.88339
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales            0.26802
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales                  0.28582
## D_0__Bacteria.D_1__Firmicutes.__.__                                                    0.04542
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia.D_3__Fusobacteriales                0.02287
## D_0__Bacteria.D_1__Lentisphaerae.D_2__Lentisphaeria.D_3__Victivallales                 0.99628
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales       0.03570
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.__                               NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales     0.15701
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Aeromonadales          0.00961
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales  0.15277
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales      0.05285
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pasteurellales         0.85034
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pseudomonadales        0.90895
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales                   0.99871
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales                   0.27986
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39                    0.22751
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Opitutales                    NA
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Verrucomicrobiales            NA
##                                                                                         
## (Intercept)                                                                             
## AGE_CONSENT                                                                           **
## ANT_BMI                                                                                 
## PMRC_LAB_TRIG                                                                           
## PMRC_LAB_HDLCHOL                                                                        
## BP_SYSTOLIC_23                                                                          
## BP_DIASTOLIC_23                                                                         
## PMRC_LAB_GLU                                                                          * 
## PMRC_LAB_GH                                                                             
## ANT_MEAS_WAIST_CM                                                                       
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria.D_3__Methanobacteriales            
## D_0__Archaea.D_1__Euryarchaeota.D_2__Thermoplasmata.D_3__Methanomassiliicoccales        
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales              
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Bifidobacteriales          **
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Corynebacteriales            
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Micrococcales                
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales             
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales                    
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Flavobacteriales                 
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Sphingobacteriales               
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales        . 
## D_0__Bacteria.D_1__Epsilonbacteraeota.D_2__Campylobacteria.D_3__Campylobacterales       
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales                              
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales                         
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales                        
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.__                                        
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales             
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales                   
## D_0__Bacteria.D_1__Firmicutes.__.__                                                   * 
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia.D_3__Fusobacteriales               * 
## D_0__Bacteria.D_1__Lentisphaerae.D_2__Lentisphaeria.D_3__Victivallales                  
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales      * 
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.__                           
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales      
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Aeromonadales         **
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales   
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales     . 
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pasteurellales          
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pseudomonadales         
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales                    
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales                    
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39                     
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Opitutales                
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Verrucomicrobiales        
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 167.07  on 120  degrees of freedom
## Residual deviance:  74.70  on  81  degrees of freedom
##   (167 observations deleted due to missingness)
## AIC: 154.7
## 
## Number of Fisher Scoring iterations: 18
#Male
# the code below checks the sum of all numeric cols and removes any cols that sum to zero
colsums_male <- colSums(Filter(is.numeric,merged.table_male))
zero_cols <- names(colsums_male[colsums_male==0 & !is.na(colsums_male)])
# re-define merged.tale without cols that sum to zero
merged.table_male <- merged.table_male %>% select(-one_of(zero_cols))

#Female
# the code below checks the sum of all numeric cols and removes any cols that sum to zero
colsums_female <- colSums(Filter(is.numeric,merged.table_female))
zero_cols <- names(colsums_female[colsums_female==0 & !is.na(colsums_female)])
# re-define merged.tale without cols that sum to zero
merged.table_female <- merged.table_female %>% select(-one_of(zero_cols))

#Correlation test

multi_assoc <- function(mdf,exp_vars, res_vars, p.zeros=.25,adj.zero=TRUE,method, inc.zeros=TRUE, run_ratio = TRUE){
  #Arguments:
  # mdf - dataframe where the explanitory and response variables are as columns and subjects are rows
  # exp_vars - a vector of numbers that indicate the explanitory variable cols in mdf 
  # res_vars - a vector of numbers that indicate the response variable cols in mdf
  # p.zeros - the max amount of zeros in a singe variable that will be tolerated (expressed as a percent)
  # this taxa has to be 25% present in all samples to run the analysis.
  # adj.zeros - add a small value to each datapoint (0.1% of the variable average) to allow for divide by zero
  # add small number, so it's close to 0 but has some values (if running correlation with 0, causes problems)
  # method - 'spearman', 'pearson'
  # spearman brings values high to low [ranking]; whereas pearson uses the actual values; spearman corrects/reduces variation but p value less significant.
  # inc.zeros - TRUE = include all zeros in exp_vars for analysis. FALSE = replace all zeros wtih NA
  # run_ration - TRUE = it will run correlations for every exp_var1:exp_var2 combination to the response variable. If not "TRUE", will only run correlations with exp_var1 vs res_var
  
  
  
  # modification of multi_assoc(method = 'spearman', ). Only divides and multiplys explanitory variables
  if (inc.zeros==FALSE){
    mdf[,exp_vars] <- apply(mdf[,exp_vars], 2, function(x) ifelse(x == 0, NA, x))
  }
  mdf$None <- c(rep(1,nrow(mdf)))
  exp_vars <- c(exp_vars,match('None', colnames(mdf)))
  d <- list()
  n <- 0
  t=1
  col_headers <- c("Explanitory_var1","Explanitory_var2","Response_var", "Estimate", "c.Pval", "Rsq", 'r.Pval')
  if(adj.zero == TRUE){ #check to see if adjustment was specified
    adj=1
  }else{
    adj=0
  }
  for (i in exp_vars[-length(exp_vars)]) { #for every exp variable. This excludes the "None" column added in line above
    if ((length(which(mdf[,i]==0|is.na(mdf[,i])==TRUE))<p.zeros*length(mdf[,i])) & (is.numeric(mdf[,i])==TRUE)){ # if the percent of zeros in exp var is less than the specified p.zero threshold, continue, else skip exp var
      if (run_ratio == TRUE){
        list2 <- exp_vars[-match(i, exp_vars)] #makes a list of all variables except for "i" variable to loop over (for divide only, see multiply below)
      } else {
        list2 <- 'None'
      }
      for (j in list2){
        if ((length(which(mdf[,j]==0|is.na(mdf[,j])==TRUE))<p.zeros*length(mdf[,j])) & (is.numeric(mdf[,j])==TRUE)){ #check to see if comparison exp var meets p.zero threshold
          for (x in res_vars){ #loops over every response variable
            #run tests
            z <- (mdf[,i]+adj*(0.001*mean(mdf[,i],na.rm = T)))/(mdf[,j]+adj*(0.001*mean(mdf[,j],na.rm = T)))
            z[is.infinite(z)] <- NA
            y <- mdf[,x]
            tmp <- cor.test(y, z, method = method)
            reg <- summary(lm(y~z))
            tmp_df <- data.frame(
              colnames(mdf[i]),
              colnames(mdf[j]),
              colnames(mdf[x]),
              as.numeric(tmp[4]), 
              as.numeric(tmp[3]),
              as.numeric(reg$r.squared),
              as.numeric(try(pf(reg$fstatistic[1],reg$fstatistic[2],reg$fstatistic[3], lower.tail = F),silent = T)),
              stringsAsFactors = FALSE)
            n <- n+1
            d[[n]] <- tmp_df
          }
        }
      }
    }
    if (t > (length(exp_vars)/100)){ # prints status as a percentage
      print(paste(match(i,exp_vars)/length(exp_vars)*100,"%"))
      t=1
    }else{
      t=t+1
    }
  }
  tmp_results <- do.call(rbind,d)
  colnames(tmp_results) <- col_headers
  tmp_results <- as_data_frame(tmp_results)
  tmp_results$c.fdr <- p.adjust(tmp_results$c.Pval)
  cp <- match("c.Pval", colnames(tmp_results))
  tmp_results <- tmp_results[,c(1:cp, ncol(tmp_results),(cp+1):(ncol(tmp_results)-1))]
  tmp_results$r.fdr <- p.adjust(tmp_results$r.Pval)
  multi_corr_tbl <- tmp_results[order(tmp_results$c.Pval, decreasing = F),]
  rownames(multi_corr_tbl) <- c(1:nrow(multi_corr_tbl))
  multi_corr_tbl$index <- c(1:nrow(multi_corr_tbl))
  if (run_ratio != TRUE){
    multi_corr_tbl <- multi_corr_tbl[,-2]
  }
  return(multi_corr_tbl)
}

#####################################
#####################################

plot_comprsn <- function (data_tbl,comp_tbl,row,color.by='All samples'){
  #Arguments:
  # data_tbl - dataframe where the explanitory and response variables are as columns and subjects are rows (same df used in multi_pred_cor())
  # comp_tbl - comparison table, this is the output of multi_pred_cor()
  # row - the row of the comp_tbl you want to plot (row 1 is the most significant correlation)
  # color.by - the col of data_table to use as input for aes(color =). Must specify the col with $.
  
  
  
  
  if (colnames(comp_tbl[2]) != "Explanitory_var2"){
    tops <- c(comp_tbl[[row,1]], "", comp_tbl[[row,2]])
    z=data_tbl[[tops[1]]]
    label <- tops[1]
  } else {
    tops <- c(comp_tbl[[row,1]], comp_tbl[[row,2]], comp_tbl[[row,3]])
    if (tops[2]=="None"){
      z=data_tbl[[tops[1]]]
      label <- tops[1]
    } else {
      z <- do.call('/',list(data_tbl[[tops[1]]],data_tbl[[tops[2]]]))
      z[is.infinite(z)] <- NA
      label <- paste(tops[1], tops[2], sep = paste("_##","/","##_"))
    }
  }
  y <- tops[3]
  data_tbl$zn <- z
  x <- 'zn'
  my.formula <- x~y
  
  if (color.by != "All samples"){
    color.by <- data_tbl[,color.by]
    colors <- scale_color_brewer(palette="Set1")
  } else {
    colors <- scale_color_manual(values = 'black')
  }
  
  plot <- data_tbl %>% ggplot(aes(x = data_tbl$zn, y = data_tbl[,y], color=color.by))+
    xlab(label)+
    ylab(tops[3])+
    geom_point()+
    colors+
    stat_cor(method = 'spearman', label.y.npc = .95)+
    geom_smooth(method=lm, se=F)
  
  return(plot)
}

#Scaterplot and heatmap ##BMI

#Try each phenotype of the disease: phe = c(6:12,14,15)
phe = c(5) #BMI
#phe = c(6) #TRIG
# phe = c(7) #HDL
# phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:51) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "3.03030303030303 %"
## [1] "6.06060606060606 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "9.09090909090909 %"
## [1] "12.1212121212121 %"
## [1] "15.1515151515152 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.1818181818182 %"
## [1] "21.2121212121212 %"
## [1] "24.2424242424242 %"
## [1] "27.2727272727273 %"
## [1] "30.3030303030303 %"
## [1] "33.3333333333333 %"
## [1] "36.3636363636364 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3939393939394 %"
## [1] "42.4242424242424 %"
## [1] "45.4545454545455 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.4848484848485 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "51.5151515151515 %"
## [1] "54.5454545454545 %"
## [1] "57.5757575757576 %"
## [1] "60.6060606060606 %"
## [1] "63.6363636363636 %"
## [1] "66.6666666666667 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.6969696969697 %"
## [1] "72.7272727272727 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.7575757575758 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "78.7878787878788 %"
## [1] "81.8181818181818 %"
## [1] "84.8484848484848 %"
## [1] "87.8787878787879 %"
## [1] "90.9090909090909 %"
## [1] "93.9393939393939 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "96.969696969697 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

taxa = c(20:51) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "3.03030303030303 %"
## [1] "6.06060606060606 %"
## [1] "9.09090909090909 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "12.1212121212121 %"
## [1] "15.1515151515152 %"
## [1] "18.1818181818182 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "21.2121212121212 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "24.2424242424242 %"
## [1] "27.2727272727273 %"
## [1] "30.3030303030303 %"
## [1] "33.3333333333333 %"
## [1] "36.3636363636364 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3939393939394 %"
## [1] "42.4242424242424 %"
## [1] "45.4545454545455 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.4848484848485 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "51.5151515151515 %"
## [1] "54.5454545454545 %"
## [1] "57.5757575757576 %"
## [1] "60.6060606060606 %"
## [1] "63.6363636363636 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "66.6666666666667 %"
## [1] "69.6969696969697 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "72.7272727272727 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.7575757575758 %"
## [1] "78.7878787878788 %"
## [1] "81.8181818181818 %"
## [1] "84.8484848484848 %"
## [1] "87.8787878787879 %"
## [1] "90.9090909090909 %"
## [1] "93.9393939393939 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "96.969696969697 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 2 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 2 rows containing non-finite values (stat_smooth).
## Warning: Removed 2 rows containing missing values (geom_point).

##TRIG

phe = c(6) #TRIG
# phe = c(7) #HDL
# phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:51) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "3.03030303030303 %"
## [1] "6.06060606060606 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "9.09090909090909 %"
## [1] "12.1212121212121 %"
## [1] "15.1515151515152 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.1818181818182 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "21.2121212121212 %"
## [1] "24.2424242424242 %"
## [1] "27.2727272727273 %"
## [1] "30.3030303030303 %"
## [1] "33.3333333333333 %"
## [1] "36.3636363636364 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3939393939394 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.4242424242424 %"
## [1] "45.4545454545455 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.4848484848485 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "51.5151515151515 %"
## [1] "54.5454545454545 %"
## [1] "57.5757575757576 %"
## [1] "60.6060606060606 %"
## [1] "63.6363636363636 %"
## [1] "66.6666666666667 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.6969696969697 %"
## [1] "72.7272727272727 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.7575757575758 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "78.7878787878788 %"
## [1] "81.8181818181818 %"
## [1] "84.8484848484848 %"
## [1] "87.8787878787879 %"
## [1] "90.9090909090909 %"
## [1] "93.9393939393939 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "96.969696969697 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 73 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 73 rows containing non-finite values (stat_smooth).
## Warning: Removed 73 rows containing missing values (geom_point).

taxa = c(20:51) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "3.03030303030303 %"
## [1] "6.06060606060606 %"
## [1] "9.09090909090909 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "12.1212121212121 %"
## [1] "15.1515151515152 %"
## [1] "18.1818181818182 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "21.2121212121212 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "24.2424242424242 %"
## [1] "27.2727272727273 %"
## [1] "30.3030303030303 %"
## [1] "33.3333333333333 %"
## [1] "36.3636363636364 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3939393939394 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.4242424242424 %"
## [1] "45.4545454545455 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.4848484848485 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "51.5151515151515 %"
## [1] "54.5454545454545 %"
## [1] "57.5757575757576 %"
## [1] "60.6060606060606 %"
## [1] "63.6363636363636 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "66.6666666666667 %"
## [1] "69.6969696969697 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "72.7272727272727 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.7575757575758 %"
## [1] "78.7878787878788 %"
## [1] "81.8181818181818 %"
## [1] "84.8484848484848 %"
## [1] "87.8787878787879 %"
## [1] "90.9090909090909 %"
## [1] "93.9393939393939 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "96.969696969697 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 88 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 88 rows containing non-finite values (stat_smooth).
## Warning: Removed 88 rows containing missing values (geom_point).

##HDL

phe = c(7) #HDL
# phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:51) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "3.03030303030303 %"
## [1] "6.06060606060606 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "9.09090909090909 %"
## [1] "12.1212121212121 %"
## [1] "15.1515151515152 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.1818181818182 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "21.2121212121212 %"
## [1] "24.2424242424242 %"
## [1] "27.2727272727273 %"
## [1] "30.3030303030303 %"
## [1] "33.3333333333333 %"
## [1] "36.3636363636364 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3939393939394 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.4242424242424 %"
## [1] "45.4545454545455 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.4848484848485 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "51.5151515151515 %"
## [1] "54.5454545454545 %"
## [1] "57.5757575757576 %"
## [1] "60.6060606060606 %"
## [1] "63.6363636363636 %"
## [1] "66.6666666666667 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.6969696969697 %"
## [1] "72.7272727272727 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.7575757575758 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "78.7878787878788 %"
## [1] "81.8181818181818 %"
## [1] "84.8484848484848 %"
## [1] "87.8787878787879 %"
## [1] "90.9090909090909 %"
## [1] "93.9393939393939 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "96.969696969697 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 74 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 74 rows containing non-finite values (stat_smooth).
## Warning: Removed 74 rows containing missing values (geom_point).

taxa = c(20:51) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "3.03030303030303 %"
## [1] "6.06060606060606 %"
## [1] "9.09090909090909 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "12.1212121212121 %"
## [1] "15.1515151515152 %"
## [1] "18.1818181818182 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "21.2121212121212 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "24.2424242424242 %"
## [1] "27.2727272727273 %"
## [1] "30.3030303030303 %"
## [1] "33.3333333333333 %"
## [1] "36.3636363636364 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3939393939394 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.4242424242424 %"
## [1] "45.4545454545455 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.4848484848485 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "51.5151515151515 %"
## [1] "54.5454545454545 %"
## [1] "57.5757575757576 %"
## [1] "60.6060606060606 %"
## [1] "63.6363636363636 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "66.6666666666667 %"
## [1] "69.6969696969697 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "72.7272727272727 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.7575757575758 %"
## [1] "78.7878787878788 %"
## [1] "81.8181818181818 %"
## [1] "84.8484848484848 %"
## [1] "87.8787878787879 %"
## [1] "90.9090909090909 %"
## [1] "93.9393939393939 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "96.969696969697 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 90 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 90 rows containing non-finite values (stat_smooth).
## Warning: Removed 90 rows containing missing values (geom_point).

##Systolic

phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:51) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "3.03030303030303 %"
## [1] "6.06060606060606 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "9.09090909090909 %"
## [1] "12.1212121212121 %"
## [1] "15.1515151515152 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.1818181818182 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "21.2121212121212 %"
## [1] "24.2424242424242 %"
## [1] "27.2727272727273 %"
## [1] "30.3030303030303 %"
## [1] "33.3333333333333 %"
## [1] "36.3636363636364 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3939393939394 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.4242424242424 %"
## [1] "45.4545454545455 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.4848484848485 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "51.5151515151515 %"
## [1] "54.5454545454545 %"
## [1] "57.5757575757576 %"
## [1] "60.6060606060606 %"
## [1] "63.6363636363636 %"
## [1] "66.6666666666667 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.6969696969697 %"
## [1] "72.7272727272727 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.7575757575758 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "78.7878787878788 %"
## [1] "81.8181818181818 %"
## [1] "84.8484848484848 %"
## [1] "87.8787878787879 %"
## [1] "90.9090909090909 %"
## [1] "93.9393939393939 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "96.969696969697 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

taxa = c(20:51) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "3.03030303030303 %"
## [1] "6.06060606060606 %"
## [1] "9.09090909090909 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "12.1212121212121 %"
## [1] "15.1515151515152 %"
## [1] "18.1818181818182 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "21.2121212121212 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "24.2424242424242 %"
## [1] "27.2727272727273 %"
## [1] "30.3030303030303 %"
## [1] "33.3333333333333 %"
## [1] "36.3636363636364 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3939393939394 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.4242424242424 %"
## [1] "45.4545454545455 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.4848484848485 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "51.5151515151515 %"
## [1] "54.5454545454545 %"
## [1] "57.5757575757576 %"
## [1] "60.6060606060606 %"
## [1] "63.6363636363636 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "66.6666666666667 %"
## [1] "69.6969696969697 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "72.7272727272727 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.7575757575758 %"
## [1] "78.7878787878788 %"
## [1] "81.8181818181818 %"
## [1] "84.8484848484848 %"
## [1] "87.8787878787879 %"
## [1] "90.9090909090909 %"
## [1] "93.9393939393939 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "96.969696969697 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

##Diastolic

phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:51) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "3.03030303030303 %"
## [1] "6.06060606060606 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "9.09090909090909 %"
## [1] "12.1212121212121 %"
## [1] "15.1515151515152 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.1818181818182 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "21.2121212121212 %"
## [1] "24.2424242424242 %"
## [1] "27.2727272727273 %"
## [1] "30.3030303030303 %"
## [1] "33.3333333333333 %"
## [1] "36.3636363636364 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3939393939394 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.4242424242424 %"
## [1] "45.4545454545455 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.4848484848485 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "51.5151515151515 %"
## [1] "54.5454545454545 %"
## [1] "57.5757575757576 %"
## [1] "60.6060606060606 %"
## [1] "63.6363636363636 %"
## [1] "66.6666666666667 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.6969696969697 %"
## [1] "72.7272727272727 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.7575757575758 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "78.7878787878788 %"
## [1] "81.8181818181818 %"
## [1] "84.8484848484848 %"
## [1] "87.8787878787879 %"
## [1] "90.9090909090909 %"
## [1] "93.9393939393939 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "96.969696969697 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

taxa = c(20:51) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "3.03030303030303 %"
## [1] "6.06060606060606 %"
## [1] "9.09090909090909 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "12.1212121212121 %"
## [1] "15.1515151515152 %"
## [1] "18.1818181818182 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "21.2121212121212 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "24.2424242424242 %"
## [1] "27.2727272727273 %"
## [1] "30.3030303030303 %"
## [1] "33.3333333333333 %"
## [1] "36.3636363636364 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3939393939394 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.4242424242424 %"
## [1] "45.4545454545455 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.4848484848485 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "51.5151515151515 %"
## [1] "54.5454545454545 %"
## [1] "57.5757575757576 %"
## [1] "60.6060606060606 %"
## [1] "63.6363636363636 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "66.6666666666667 %"
## [1] "69.6969696969697 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "72.7272727272727 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.7575757575758 %"
## [1] "78.7878787878788 %"
## [1] "81.8181818181818 %"
## [1] "84.8484848484848 %"
## [1] "87.8787878787879 %"
## [1] "90.9090909090909 %"
## [1] "93.9393939393939 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "96.969696969697 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

##GLU

phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:51) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "3.03030303030303 %"
## [1] "6.06060606060606 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "9.09090909090909 %"
## [1] "12.1212121212121 %"
## [1] "15.1515151515152 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.1818181818182 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "21.2121212121212 %"
## [1] "24.2424242424242 %"
## [1] "27.2727272727273 %"
## [1] "30.3030303030303 %"
## [1] "33.3333333333333 %"
## [1] "36.3636363636364 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3939393939394 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.4242424242424 %"
## [1] "45.4545454545455 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.4848484848485 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "51.5151515151515 %"
## [1] "54.5454545454545 %"
## [1] "57.5757575757576 %"
## [1] "60.6060606060606 %"
## [1] "63.6363636363636 %"
## [1] "66.6666666666667 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.6969696969697 %"
## [1] "72.7272727272727 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.7575757575758 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "78.7878787878788 %"
## [1] "81.8181818181818 %"
## [1] "84.8484848484848 %"
## [1] "87.8787878787879 %"
## [1] "90.9090909090909 %"
## [1] "93.9393939393939 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "96.969696969697 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 74 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 74 rows containing non-finite values (stat_smooth).
## Warning: Removed 74 rows containing missing values (geom_point).

taxa = c(20:51) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "3.03030303030303 %"
## [1] "6.06060606060606 %"
## [1] "9.09090909090909 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "12.1212121212121 %"
## [1] "15.1515151515152 %"
## [1] "18.1818181818182 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "21.2121212121212 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "24.2424242424242 %"
## [1] "27.2727272727273 %"
## [1] "30.3030303030303 %"
## [1] "33.3333333333333 %"
## [1] "36.3636363636364 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3939393939394 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.4242424242424 %"
## [1] "45.4545454545455 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.4848484848485 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "51.5151515151515 %"
## [1] "54.5454545454545 %"
## [1] "57.5757575757576 %"
## [1] "60.6060606060606 %"
## [1] "63.6363636363636 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "66.6666666666667 %"
## [1] "69.6969696969697 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "72.7272727272727 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.7575757575758 %"
## [1] "78.7878787878788 %"
## [1] "81.8181818181818 %"
## [1] "84.8484848484848 %"
## [1] "87.8787878787879 %"
## [1] "90.9090909090909 %"
## [1] "93.9393939393939 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "96.969696969697 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 90 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 90 rows containing non-finite values (stat_smooth).
## Warning: Removed 90 rows containing missing values (geom_point).

##GH

phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:51) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "3.03030303030303 %"
## [1] "6.06060606060606 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "9.09090909090909 %"
## [1] "12.1212121212121 %"
## [1] "15.1515151515152 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.1818181818182 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "21.2121212121212 %"
## [1] "24.2424242424242 %"
## [1] "27.2727272727273 %"
## [1] "30.3030303030303 %"
## [1] "33.3333333333333 %"
## [1] "36.3636363636364 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3939393939394 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.4242424242424 %"
## [1] "45.4545454545455 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.4848484848485 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "51.5151515151515 %"
## [1] "54.5454545454545 %"
## [1] "57.5757575757576 %"
## [1] "60.6060606060606 %"
## [1] "63.6363636363636 %"
## [1] "66.6666666666667 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.6969696969697 %"
## [1] "72.7272727272727 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.7575757575758 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "78.7878787878788 %"
## [1] "81.8181818181818 %"
## [1] "84.8484848484848 %"
## [1] "87.8787878787879 %"
## [1] "90.9090909090909 %"
## [1] "93.9393939393939 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "96.969696969697 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 74 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 74 rows containing non-finite values (stat_smooth).
## Warning: Removed 74 rows containing missing values (geom_point).

taxa = c(20:51) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "3.03030303030303 %"
## [1] "6.06060606060606 %"
## [1] "9.09090909090909 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "12.1212121212121 %"
## [1] "15.1515151515152 %"
## [1] "18.1818181818182 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "21.2121212121212 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "24.2424242424242 %"
## [1] "27.2727272727273 %"
## [1] "30.3030303030303 %"
## [1] "33.3333333333333 %"
## [1] "36.3636363636364 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3939393939394 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.4242424242424 %"
## [1] "45.4545454545455 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.4848484848485 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "51.5151515151515 %"
## [1] "54.5454545454545 %"
## [1] "57.5757575757576 %"
## [1] "60.6060606060606 %"
## [1] "63.6363636363636 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "66.6666666666667 %"
## [1] "69.6969696969697 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "72.7272727272727 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.7575757575758 %"
## [1] "78.7878787878788 %"
## [1] "81.8181818181818 %"
## [1] "84.8484848484848 %"
## [1] "87.8787878787879 %"
## [1] "90.9090909090909 %"
## [1] "93.9393939393939 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "96.969696969697 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 90 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 90 rows containing non-finite values (stat_smooth).
## Warning: Removed 90 rows containing missing values (geom_point).

##AGE

phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:51) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "3.03030303030303 %"
## [1] "6.06060606060606 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "9.09090909090909 %"
## [1] "12.1212121212121 %"
## [1] "15.1515151515152 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.1818181818182 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "21.2121212121212 %"
## [1] "24.2424242424242 %"
## [1] "27.2727272727273 %"
## [1] "30.3030303030303 %"
## [1] "33.3333333333333 %"
## [1] "36.3636363636364 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3939393939394 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.4242424242424 %"
## [1] "45.4545454545455 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.4848484848485 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "51.5151515151515 %"
## [1] "54.5454545454545 %"
## [1] "57.5757575757576 %"
## [1] "60.6060606060606 %"
## [1] "63.6363636363636 %"
## [1] "66.6666666666667 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.6969696969697 %"
## [1] "72.7272727272727 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.7575757575758 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "78.7878787878788 %"
## [1] "81.8181818181818 %"
## [1] "84.8484848484848 %"
## [1] "87.8787878787879 %"
## [1] "90.9090909090909 %"
## [1] "93.9393939393939 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "96.969696969697 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

taxa = c(20:51) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "3.03030303030303 %"
## [1] "6.06060606060606 %"
## [1] "9.09090909090909 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "12.1212121212121 %"
## [1] "15.1515151515152 %"
## [1] "18.1818181818182 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "21.2121212121212 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "24.2424242424242 %"
## [1] "27.2727272727273 %"
## [1] "30.3030303030303 %"
## [1] "33.3333333333333 %"
## [1] "36.3636363636364 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3939393939394 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.4242424242424 %"
## [1] "45.4545454545455 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.4848484848485 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "51.5151515151515 %"
## [1] "54.5454545454545 %"
## [1] "57.5757575757576 %"
## [1] "60.6060606060606 %"
## [1] "63.6363636363636 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "66.6666666666667 %"
## [1] "69.6969696969697 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "72.7272727272727 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.7575757575758 %"
## [1] "78.7878787878788 %"
## [1] "81.8181818181818 %"
## [1] "84.8484848484848 %"
## [1] "87.8787878787879 %"
## [1] "90.9090909090909 %"
## [1] "93.9393939393939 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "96.969696969697 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

##Waist

phe = c(14) #Waist


taxa = c(20:51) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "3.03030303030303 %"
## [1] "6.06060606060606 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "9.09090909090909 %"
## [1] "12.1212121212121 %"
## [1] "15.1515151515152 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.1818181818182 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "21.2121212121212 %"
## [1] "24.2424242424242 %"
## [1] "27.2727272727273 %"
## [1] "30.3030303030303 %"
## [1] "33.3333333333333 %"
## [1] "36.3636363636364 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3939393939394 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.4242424242424 %"
## [1] "45.4545454545455 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.4848484848485 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "51.5151515151515 %"
## [1] "54.5454545454545 %"
## [1] "57.5757575757576 %"
## [1] "60.6060606060606 %"
## [1] "63.6363636363636 %"
## [1] "66.6666666666667 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.6969696969697 %"
## [1] "72.7272727272727 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.7575757575758 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "78.7878787878788 %"
## [1] "81.8181818181818 %"
## [1] "84.8484848484848 %"
## [1] "87.8787878787879 %"
## [1] "90.9090909090909 %"
## [1] "93.9393939393939 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "96.969696969697 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

taxa = c(20:51) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "3.03030303030303 %"
## [1] "6.06060606060606 %"
## [1] "9.09090909090909 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "12.1212121212121 %"
## [1] "15.1515151515152 %"
## [1] "18.1818181818182 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "21.2121212121212 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "24.2424242424242 %"
## [1] "27.2727272727273 %"
## [1] "30.3030303030303 %"
## [1] "33.3333333333333 %"
## [1] "36.3636363636364 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3939393939394 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.4242424242424 %"
## [1] "45.4545454545455 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.4848484848485 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "51.5151515151515 %"
## [1] "54.5454545454545 %"
## [1] "57.5757575757576 %"
## [1] "60.6060606060606 %"
## [1] "63.6363636363636 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "66.6666666666667 %"
## [1] "69.6969696969697 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "72.7272727272727 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.7575757575758 %"
## [1] "78.7878787878788 %"
## [1] "81.8181818181818 %"
## [1] "84.8484848484848 %"
## [1] "87.8787878787879 %"
## [1] "90.9090909090909 %"
## [1] "93.9393939393939 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "96.969696969697 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

#Heatmap_level4

#Male
# Visualizing the correlation in heatmap [30x30]; try with class x class- level 3
library(corrplot)
res = cor.mtest(merged.table_male[,c(5:11,13,14,20:51)], conf.level = 0.95, rm.na = T)
## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero
Correlation <- round(cor(merged.table_male[,c(5:11,13,14,20:51)],method = "spearman", use="complete.obs"), 2)
## Warning in cor(merged.table_male[, c(5:11, 13, 14, 20:51)], method =
## "spearman", : the standard deviation is zero
corrplot(Correlation, method = "ellipse", tl.col = "black", type = 'upper', tl.cex = 0.4, cl.cex = 0.4, p.mat = res$p, insig = "blank", sig.level = 0.05) #heatmap; blue=neg corr; red=pos corr

#Female
# Visualizing the correlation in heatmap [30x30]; try with class x class- level 3
library(corrplot)
res = cor.mtest(merged.table_female[,c(5:11,13,14,20:51)], conf.level = 0.95, rm.na = T)
## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero
Correlation <- round(cor(merged.table_female[,c(5:11,13,14,20:51)],method = "spearman", use="complete.obs"), 2)
## Warning in cor(merged.table_female[, c(5:11, 13, 14, 20:51)], method =
## "spearman", : the standard deviation is zero
corrplot(Correlation, method = "ellipse", tl.col = "black", type = 'upper', tl.cex = 0.4, cl.cex = 0.4, p.mat = res$p, insig = "blank", sig.level = 0.05) #heatmap; blue=neg corr; red=pos corr

#Read dataframes_level5_family

#ASVs <- read_qza("microbiome_data/filtered/table_filt.qza") #Gives me an error so I commented out.
taxa_table <- read.csv("level-5_family_taxtable_clean.csv", header=T) # csv obtained from /Users/giovanna/OneDrive - UW-Madison/Rotations/3 Denu-Rey/SHOW data/microbiome_data/taxa/taxa_barplot.qza
taxa_table = taxa_table[,1:75] #all rows, from columns 1 to 112
taxa_ra <- sweep(taxa_table[,2:ncol(taxa_table)],1,rowSums(taxa_table[,2:ncol(taxa_table)]),"/") #relative abundance - normalization of sample reads
taxa_ra$index = taxa_table$index
merged.table_family <- merge(MetS_feature, taxa_ra, by.x="16S_ID", by.y="index")

merged.table_male <- merged.table_family %>%
  filter(GENDER == "[1] Male")
merged.table_female <- merged.table_family %>%
  filter(GENDER == "[2] Female")

#Regression
MetS_feature$MetS <- ifelse((MetS_feature$MetS.binary == 1) | (MetS_feature$gh.binary ==1), 1, 0)
reg_data_family <- merged.table_family %>% select(MetS,AGE_CONSENT, ANT_BMI, PMRC_LAB_TRIG, PMRC_LAB_HDLCHOL, BP_SYSTOLIC_23, BP_DIASTOLIC_23, PMRC_LAB_GLU, PMRC_LAB_GH, ANT_MEAS_WAIST_CM, starts_with("D_0__"))
lmod <- glm(MetS ~ ., family = "binomial", data = reg_data_family)
## Warning: glm.fit: algorithm did not converge
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
summary(lmod)
## 
## Call:
## glm(formula = MetS ~ ., family = "binomial", data = reg_data_family)
## 
## Deviance Residuals: 
##        Min          1Q      Median          3Q         Max  
## -1.973e-05  -2.892e-06  -2.110e-08   2.409e-06   2.716e-05  
## 
## Coefficients: (8 not defined because of singularities)
##                                                                                                                                        Estimate
## (Intercept)                                                                                                                           9.295e+02
## AGE_CONSENT                                                                                                                          -2.792e+00
## ANT_BMI                                                                                                                               1.765e+00
## PMRC_LAB_TRIG                                                                                                                         2.005e-01
## PMRC_LAB_HDLCHOL                                                                                                                     -4.659e-01
## BP_SYSTOLIC_23                                                                                                                        1.950e+00
## BP_DIASTOLIC_23                                                                                                                      -1.399e+00
## PMRC_LAB_GLU                                                                                                                          6.920e-01
## PMRC_LAB_GH                                                                                                                           4.136e+01
## ANT_MEAS_WAIST_CM                                                                                                                    -3.022e+00
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria.D_3__Methanobacteriales.D_4__Methanobacteriaceae                                -1.122e+03
## D_0__Archaea.D_1__Euryarchaeota.D_2__Thermoplasmata.D_3__Methanomassiliicoccales.D_4__Methanomassiliicoccaceae                        1.771e+05
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales.D_4__Actinomycetaceae                                     -9.529e+03
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Bifidobacteriales.D_4__Bifidobacteriaceae                                 -3.836e+03
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Corynebacteriales.D_4__Corynebacteriaceae                                  4.450e+07
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Micrococcales.D_4__Micrococcaceae                                         -1.338e+06
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Atopobiaceae                                        -2.202e+05
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Coriobacteriaceae                                    9.764e+03
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Coriobacteriales.Incertae.Sedis                     -2.599e+04
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae                                      1.440e+04
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__uncultured                                           2.170e+05
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Bacteroidaceae                                             -8.176e+02
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Barnesiellaceae                                            -5.753e+03
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Dysgonomonadaceae                                          -1.187e+04
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Marinifilaceae                                              1.713e+04
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae                                              6.449e+03
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Porphyromonadaceae                                         -8.640e+04
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae                                             -4.203e+02
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae                                              -8.322e+02
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Tannerellaceae                                             -1.410e+03
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__uncultured                                                 -3.315e+04
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.__                                                               2.825e+04
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Flavobacteriales.D_4__Flavobacteriaceae                                       -6.014e+05
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Sphingobacteriales.D_4__Sphingobacteriaceae                                           NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__Candidatus.Gastranaerophilales.bacterium.Zag_111         NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__Clostridium.sp..CAG.306                           1.028e+07
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__uncultured.bacterium                              1.621e+05
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.__                                                     4.408e+04
## D_0__Bacteria.D_1__Epsilonbacteraeota.D_2__Campylobacteria.D_3__Campylobacterales.D_4__Campylobacteraceae                             1.670e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales.D_4__Family.XI                                                             1.816e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales.D_4__Staphylococcaceae                                                     4.079e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Carnobacteriaceae                                               -6.464e+04
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Enterococcaceae                                                 -4.128e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Lactobacillaceae                                                -4.342e+02
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Leuconostocaceae                                                -6.730e+04
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Streptococcaceae                                                 2.214e+02
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae                                            -3.710e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiaceae.1                                                9.501e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group                                   5.538e+04
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Defluviitaleaceae                                               1.360e+04
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Eubacteriaceae                                                  1.672e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI                                                       2.499e+04
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII                                                    -7.090e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae                                                -1.017e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptococcaceae                                                 -1.817e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae                                          -3.467e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae                                                -1.139e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.__                                                                   1.565e+04
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.__.__                                                                                  -3.066e+04
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae                                 -3.446e+02
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Acidaminococcaceae                                        -1.652e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae                                           -9.438e+02
## D_0__Bacteria.D_1__Firmicutes.__.__.__                                                                                                1.864e+05
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia.D_3__Fusobacteriales.D_4__Fusobacteriaceae                                         1.603e+04
## D_0__Bacteria.D_1__Lentisphaerae.D_2__Lentisphaeria.D_3__Victivallales.D_4__Victivallaceae                                           -1.106e+05
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured                                     -2.654e+04
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.__.__                                                                             NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae                          -5.143e+03
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Aeromonadales.D_4__Succinivibrionaceae                               -2.522e+04
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae                          -1.467e+03
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae                            -1.524e+03
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pasteurellales.D_4__Pasteurellaceae                                  -1.206e+04
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pseudomonadales.D_4__Pseudomonadaceae                                -2.895e+06
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales.D_4__Synergistaceae                                             -5.786e+03
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales.D_4__gut.metagenome                                                     NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales.D_4__uncultured.organism                                        -6.409e+04
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__Firmicutes.bacterium.CAG.822                                -5.906e+05
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__gut.metagenome                                               1.094e+05
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__uncultured.bacterium                                        -1.082e+05
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__uncultured.bacterium.adhufec202                                     NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__unidentified.rumen.bacterium.RF39                                   NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.__                                                                4.723e+04
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Opitutales.D_4__Puniceicoccaceae                                               NA
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Verrucomicrobiales.D_4__Akkermansiaceae                                        NA
##                                                                                                                                      Std. Error
## (Intercept)                                                                                                                           3.362e+06
## AGE_CONSENT                                                                                                                           4.754e+03
## ANT_BMI                                                                                                                               1.519e+04
## PMRC_LAB_TRIG                                                                                                                         5.303e+02
## PMRC_LAB_HDLCHOL                                                                                                                      2.997e+03
## BP_SYSTOLIC_23                                                                                                                        5.122e+03
## BP_DIASTOLIC_23                                                                                                                       8.027e+03
## PMRC_LAB_GLU                                                                                                                          2.082e+03
## PMRC_LAB_GH                                                                                                                           1.709e+05
## ANT_MEAS_WAIST_CM                                                                                                                     8.482e+03
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria.D_3__Methanobacteriales.D_4__Methanobacteriaceae                                 1.088e+07
## D_0__Archaea.D_1__Euryarchaeota.D_2__Thermoplasmata.D_3__Methanomassiliicoccales.D_4__Methanomassiliicoccaceae                        2.885e+09
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales.D_4__Actinomycetaceae                                      1.190e+08
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Bifidobacteriales.D_4__Bifidobacteriaceae                                  5.301e+06
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Corynebacteriales.D_4__Corynebacteriaceae                                  7.048e+10
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Micrococcales.D_4__Micrococcaceae                                          4.209e+09
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Atopobiaceae                                         5.449e+08
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Coriobacteriaceae                                    1.682e+07
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Coriobacteriales.Incertae.Sedis                      1.634e+08
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae                                      6.579e+07
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__uncultured                                           6.005e+08
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Bacteroidaceae                                              3.123e+06
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Barnesiellaceae                                             1.366e+07
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Dysgonomonadaceae                                           3.084e+07
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Marinifilaceae                                              6.005e+07
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae                                              4.093e+07
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Porphyromonadaceae                                          4.855e+08
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae                                              3.316e+06
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae                                               2.851e+06
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Tannerellaceae                                              4.689e+06
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__uncultured                                                  7.316e+07
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.__                                                               6.074e+07
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Flavobacteriales.D_4__Flavobacteriaceae                                        1.023e+09
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Sphingobacteriales.D_4__Sphingobacteriaceae                                           NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__Candidatus.Gastranaerophilales.bacterium.Zag_111         NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__Clostridium.sp..CAG.306                           2.723e+10
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__uncultured.bacterium                              8.819e+08
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.__                                                     3.984e+08
## D_0__Bacteria.D_1__Epsilonbacteraeota.D_2__Campylobacteria.D_3__Campylobacterales.D_4__Campylobacteraceae                             4.421e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales.D_4__Family.XI                                                             9.198e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales.D_4__Staphylococcaceae                                                     2.275e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Carnobacteriaceae                                                1.459e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Enterococcaceae                                                  8.947e+07
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Lactobacillaceae                                                 6.822e+06
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Leuconostocaceae                                                 2.244e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Streptococcaceae                                                 4.641e+06
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae                                             1.146e+07
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiaceae.1                                                5.164e+07
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group                                   1.715e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Defluviitaleaceae                                               5.598e+07
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Eubacteriaceae                                                  4.344e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI                                                       2.215e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII                                                     2.129e+07
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae                                                 2.885e+06
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptococcaceae                                                  4.566e+07
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae                                           1.437e+07
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae                                                 2.819e+06
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.__                                                                   1.344e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.__.__                                                                                   1.272e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae                                  3.056e+06
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Acidaminococcaceae                                         5.349e+06
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae                                            3.046e+06
## D_0__Bacteria.D_1__Firmicutes.__.__.__                                                                                                9.960e+08
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia.D_3__Fusobacteriales.D_4__Fusobacteriaceae                                         6.791e+07
## D_0__Bacteria.D_1__Lentisphaerae.D_2__Lentisphaeria.D_3__Victivallales.D_4__Victivallaceae                                            1.353e+09
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured                                      2.072e+08
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.__.__                                                                             NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae                           2.148e+07
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Aeromonadales.D_4__Succinivibrionaceae                                1.901e+08
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae                           7.008e+06
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae                             3.593e+06
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pasteurellales.D_4__Pasteurellaceae                                   2.909e+07
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pseudomonadales.D_4__Pseudomonadaceae                                 7.311e+09
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales.D_4__Synergistaceae                                              4.736e+07
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales.D_4__gut.metagenome                                                     NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales.D_4__uncultured.organism                                         1.771e+08
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__Firmicutes.bacterium.CAG.822                                 2.954e+09
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__gut.metagenome                                               2.264e+08
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__uncultured.bacterium                                         5.634e+08
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__uncultured.bacterium.adhufec202                                     NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__unidentified.rumen.bacterium.RF39                                   NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.__                                                                2.396e+08
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Opitutales.D_4__Puniceicoccaceae                                               NA
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Verrucomicrobiales.D_4__Akkermansiaceae                                        NA
##                                                                                                                                      z value
## (Intercept)                                                                                                                            0.000
## AGE_CONSENT                                                                                                                           -0.001
## ANT_BMI                                                                                                                                0.000
## PMRC_LAB_TRIG                                                                                                                          0.000
## PMRC_LAB_HDLCHOL                                                                                                                       0.000
## BP_SYSTOLIC_23                                                                                                                         0.000
## BP_DIASTOLIC_23                                                                                                                        0.000
## PMRC_LAB_GLU                                                                                                                           0.000
## PMRC_LAB_GH                                                                                                                            0.000
## ANT_MEAS_WAIST_CM                                                                                                                      0.000
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria.D_3__Methanobacteriales.D_4__Methanobacteriaceae                                  0.000
## D_0__Archaea.D_1__Euryarchaeota.D_2__Thermoplasmata.D_3__Methanomassiliicoccales.D_4__Methanomassiliicoccaceae                         0.000
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales.D_4__Actinomycetaceae                                       0.000
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Bifidobacteriales.D_4__Bifidobacteriaceae                                  -0.001
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Corynebacteriales.D_4__Corynebacteriaceae                                   0.001
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Micrococcales.D_4__Micrococcaceae                                           0.000
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Atopobiaceae                                          0.000
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Coriobacteriaceae                                     0.001
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Coriobacteriales.Incertae.Sedis                       0.000
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae                                       0.000
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__uncultured                                            0.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Bacteroidaceae                                               0.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Barnesiellaceae                                              0.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Dysgonomonadaceae                                            0.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Marinifilaceae                                               0.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae                                               0.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Porphyromonadaceae                                           0.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae                                               0.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae                                                0.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Tannerellaceae                                               0.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__uncultured                                                   0.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.__                                                                0.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Flavobacteriales.D_4__Flavobacteriaceae                                        -0.001
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Sphingobacteriales.D_4__Sphingobacteriaceae                                        NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__Candidatus.Gastranaerophilales.bacterium.Zag_111      NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__Clostridium.sp..CAG.306                            0.000
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__uncultured.bacterium                               0.000
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.__                                                      0.000
## D_0__Bacteria.D_1__Epsilonbacteraeota.D_2__Campylobacteria.D_3__Campylobacterales.D_4__Campylobacteraceae                              0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales.D_4__Family.XI                                                              0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales.D_4__Staphylococcaceae                                                      0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Carnobacteriaceae                                                 0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Enterococcaceae                                                   0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Lactobacillaceae                                                  0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Leuconostocaceae                                                  0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Streptococcaceae                                                  0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae                                              0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiaceae.1                                                 0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group                                    0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Defluviitaleaceae                                                0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Eubacteriaceae                                                   0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI                                                        0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII                                                      0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae                                                  0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptococcaceae                                                   0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae                                            0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae                                                  0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.__                                                                    0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.__.__                                                                                    0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae                                   0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Acidaminococcaceae                                          0.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae                                             0.000
## D_0__Bacteria.D_1__Firmicutes.__.__.__                                                                                                 0.000
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia.D_3__Fusobacteriales.D_4__Fusobacteriaceae                                          0.000
## D_0__Bacteria.D_1__Lentisphaerae.D_2__Lentisphaeria.D_3__Victivallales.D_4__Victivallaceae                                             0.000
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured                                       0.000
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.__.__                                                                          NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae                            0.000
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Aeromonadales.D_4__Succinivibrionaceae                                 0.000
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae                            0.000
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae                              0.000
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pasteurellales.D_4__Pasteurellaceae                                    0.000
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pseudomonadales.D_4__Pseudomonadaceae                                  0.000
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales.D_4__Synergistaceae                                               0.000
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales.D_4__gut.metagenome                                                  NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales.D_4__uncultured.organism                                          0.000
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__Firmicutes.bacterium.CAG.822                                  0.000
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__gut.metagenome                                                0.000
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__uncultured.bacterium                                          0.000
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__uncultured.bacterium.adhufec202                                  NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__unidentified.rumen.bacterium.RF39                                NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.__                                                                 0.000
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Opitutales.D_4__Puniceicoccaceae                                            NA
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Verrucomicrobiales.D_4__Akkermansiaceae                                     NA
##                                                                                                                                      Pr(>|z|)
## (Intercept)                                                                                                                             1.000
## AGE_CONSENT                                                                                                                             1.000
## ANT_BMI                                                                                                                                 1.000
## PMRC_LAB_TRIG                                                                                                                           1.000
## PMRC_LAB_HDLCHOL                                                                                                                        1.000
## BP_SYSTOLIC_23                                                                                                                          1.000
## BP_DIASTOLIC_23                                                                                                                         1.000
## PMRC_LAB_GLU                                                                                                                            1.000
## PMRC_LAB_GH                                                                                                                             1.000
## ANT_MEAS_WAIST_CM                                                                                                                       1.000
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria.D_3__Methanobacteriales.D_4__Methanobacteriaceae                                   1.000
## D_0__Archaea.D_1__Euryarchaeota.D_2__Thermoplasmata.D_3__Methanomassiliicoccales.D_4__Methanomassiliicoccaceae                          1.000
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales.D_4__Actinomycetaceae                                        1.000
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Bifidobacteriales.D_4__Bifidobacteriaceae                                    0.999
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Corynebacteriales.D_4__Corynebacteriaceae                                    0.999
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Micrococcales.D_4__Micrococcaceae                                            1.000
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Atopobiaceae                                           1.000
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Coriobacteriaceae                                      1.000
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Coriobacteriales.Incertae.Sedis                        1.000
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae                                        1.000
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__uncultured                                             1.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Bacteroidaceae                                                1.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Barnesiellaceae                                               1.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Dysgonomonadaceae                                             1.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Marinifilaceae                                                1.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae                                                1.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Porphyromonadaceae                                            1.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae                                                1.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae                                                 1.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Tannerellaceae                                                1.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__uncultured                                                    1.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.__                                                                 1.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Flavobacteriales.D_4__Flavobacteriaceae                                          1.000
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Sphingobacteriales.D_4__Sphingobacteriaceae                                         NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__Candidatus.Gastranaerophilales.bacterium.Zag_111       NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__Clostridium.sp..CAG.306                             1.000
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__uncultured.bacterium                                1.000
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.__                                                       1.000
## D_0__Bacteria.D_1__Epsilonbacteraeota.D_2__Campylobacteria.D_3__Campylobacterales.D_4__Campylobacteraceae                               1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales.D_4__Family.XI                                                               1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales.D_4__Staphylococcaceae                                                       1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Carnobacteriaceae                                                  1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Enterococcaceae                                                    1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Lactobacillaceae                                                   1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Leuconostocaceae                                                   1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Streptococcaceae                                                   1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae                                               1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiaceae.1                                                  1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group                                     1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Defluviitaleaceae                                                 1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Eubacteriaceae                                                    1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI                                                         1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII                                                       1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae                                                   1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptococcaceae                                                    1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae                                             1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae                                                   1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.__                                                                     1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.__.__                                                                                     1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae                                    1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Acidaminococcaceae                                           1.000
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae                                              1.000
## D_0__Bacteria.D_1__Firmicutes.__.__.__                                                                                                  1.000
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia.D_3__Fusobacteriales.D_4__Fusobacteriaceae                                           1.000
## D_0__Bacteria.D_1__Lentisphaerae.D_2__Lentisphaeria.D_3__Victivallales.D_4__Victivallaceae                                              1.000
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured                                        1.000
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.__.__                                                                           NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae                             1.000
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Aeromonadales.D_4__Succinivibrionaceae                                  1.000
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae                             1.000
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae                               1.000
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pasteurellales.D_4__Pasteurellaceae                                     1.000
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pseudomonadales.D_4__Pseudomonadaceae                                   1.000
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales.D_4__Synergistaceae                                                1.000
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales.D_4__gut.metagenome                                                   NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales.D_4__uncultured.organism                                           1.000
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__Firmicutes.bacterium.CAG.822                                   1.000
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__gut.metagenome                                                 1.000
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__uncultured.bacterium                                           1.000
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__uncultured.bacterium.adhufec202                                   NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__unidentified.rumen.bacterium.RF39                                 NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.__                                                                  1.000
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Opitutales.D_4__Puniceicoccaceae                                             NA
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Verrucomicrobiales.D_4__Akkermansiaceae                                      NA
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 1.6707e+02  on 120  degrees of freedom
## Residual deviance: 6.5603e-09  on  45  degrees of freedom
##   (167 observations deleted due to missingness)
## AIC: 152
## 
## Number of Fisher Scoring iterations: 25
#Male
# the code below checks the sum of all numeric cols and removes any cols that sum to zero
colsums_male <- colSums(Filter(is.numeric,merged.table_male))
zero_cols <- names(colsums_male[colsums_male==0 & !is.na(colsums_male)])
# re-define merged.tale without cols that sum to zero
merged.table_male <- merged.table_male %>% select(-one_of(zero_cols))

#Female
# the code below checks the sum of all numeric cols and removes any cols that sum to zero
colsums_female <- colSums(Filter(is.numeric,merged.table_female))
zero_cols <- names(colsums_female[colsums_female==0 & !is.na(colsums_female)])
# re-define merged.tale without cols that sum to zero
merged.table_female <- merged.table_female %>% select(-one_of(zero_cols))

#Correlation test

multi_assoc <- function(mdf,exp_vars, res_vars, p.zeros=.25,adj.zero=TRUE,method, inc.zeros=TRUE, run_ratio = TRUE){
  #Arguments:
  # mdf - dataframe where the explanitory and response variables are as columns and subjects are rows
  # exp_vars - a vector of numbers that indicate the explanitory variable cols in mdf 
  # res_vars - a vector of numbers that indicate the response variable cols in mdf
  # p.zeros - the max amount of zeros in a singe variable that will be tolerated (expressed as a percent)
  # this taxa has to be 25% present in all samples to run the analysis.
  # adj.zeros - add a small value to each datapoint (0.1% of the variable average) to allow for divide by zero
  # add small number, so it's close to 0 but has some values (if running correlation with 0, causes problems)
  # method - 'spearman', 'pearson'
  # spearman brings values high to low [ranking]; whereas pearson uses the actual values; spearman corrects/reduces variation but p value less significant.
  # inc.zeros - TRUE = include all zeros in exp_vars for analysis. FALSE = replace all zeros wtih NA
  # run_ration - TRUE = it will run correlations for every exp_var1:exp_var2 combination to the response variable. If not "TRUE", will only run correlations with exp_var1 vs res_var
  
  
  
  # modification of multi_assoc(method = 'spearman', ). Only divides and multiplys explanitory variables
  if (inc.zeros==FALSE){
    mdf[,exp_vars] <- apply(mdf[,exp_vars], 2, function(x) ifelse(x == 0, NA, x))
  }
  mdf$None <- c(rep(1,nrow(mdf)))
  exp_vars <- c(exp_vars,match('None', colnames(mdf)))
  d <- list()
  n <- 0
  t=1
  col_headers <- c("Explanitory_var1","Explanitory_var2","Response_var", "Estimate", "c.Pval", "Rsq", 'r.Pval')
  if(adj.zero == TRUE){ #check to see if adjustment was specified
    adj=1
  }else{
    adj=0
  }
  for (i in exp_vars[-length(exp_vars)]) { #for every exp variable. This excludes the "None" column added in line above
    if ((length(which(mdf[,i]==0|is.na(mdf[,i])==TRUE))<p.zeros*length(mdf[,i])) & (is.numeric(mdf[,i])==TRUE)){ # if the percent of zeros in exp var is less than the specified p.zero threshold, continue, else skip exp var
      if (run_ratio == TRUE){
        list2 <- exp_vars[-match(i, exp_vars)] #makes a list of all variables except for "i" variable to loop over (for divide only, see multiply below)
      } else {
        list2 <- 'None'
      }
      for (j in list2){
        if ((length(which(mdf[,j]==0|is.na(mdf[,j])==TRUE))<p.zeros*length(mdf[,j])) & (is.numeric(mdf[,j])==TRUE)){ #check to see if comparison exp var meets p.zero threshold
          for (x in res_vars){ #loops over every response variable
            #run tests
            z <- (mdf[,i]+adj*(0.001*mean(mdf[,i],na.rm = T)))/(mdf[,j]+adj*(0.001*mean(mdf[,j],na.rm = T)))
            z[is.infinite(z)] <- NA
            y <- mdf[,x]
            tmp <- cor.test(y, z, method = method)
            reg <- summary(lm(y~z))
            tmp_df <- data.frame(
              colnames(mdf[i]),
              colnames(mdf[j]),
              colnames(mdf[x]),
              as.numeric(tmp[4]), 
              as.numeric(tmp[3]),
              as.numeric(reg$r.squared),
              as.numeric(try(pf(reg$fstatistic[1],reg$fstatistic[2],reg$fstatistic[3], lower.tail = F),silent = T)),
              stringsAsFactors = FALSE)
            n <- n+1
            d[[n]] <- tmp_df
          }
        }
      }
    }
    if (t > (length(exp_vars)/100)){ # prints status as a percentage
      print(paste(match(i,exp_vars)/length(exp_vars)*100,"%"))
      t=1
    }else{
      t=t+1
    }
  }
  tmp_results <- do.call(rbind,d)
  colnames(tmp_results) <- col_headers
  tmp_results <- as_data_frame(tmp_results)
  tmp_results$c.fdr <- p.adjust(tmp_results$c.Pval)
  cp <- match("c.Pval", colnames(tmp_results))
  tmp_results <- tmp_results[,c(1:cp, ncol(tmp_results),(cp+1):(ncol(tmp_results)-1))]
  tmp_results$r.fdr <- p.adjust(tmp_results$r.Pval)
  multi_corr_tbl <- tmp_results[order(tmp_results$c.Pval, decreasing = F),]
  rownames(multi_corr_tbl) <- c(1:nrow(multi_corr_tbl))
  multi_corr_tbl$index <- c(1:nrow(multi_corr_tbl))
  if (run_ratio != TRUE){
    multi_corr_tbl <- multi_corr_tbl[,-2]
  }
  return(multi_corr_tbl)
}

#####################################
#####################################

plot_comprsn <- function (data_tbl,comp_tbl,row,color.by='All samples'){
  #Arguments:
  # data_tbl - dataframe where the explanitory and response variables are as columns and subjects are rows (same df used in multi_pred_cor())
  # comp_tbl - comparison table, this is the output of multi_pred_cor()
  # row - the row of the comp_tbl you want to plot (row 1 is the most significant correlation)
  # color.by - the col of data_table to use as input for aes(color =). Must specify the col with $.
  
  
  
  
  if (colnames(comp_tbl[2]) != "Explanitory_var2"){
    tops <- c(comp_tbl[[row,1]], "", comp_tbl[[row,2]])
    z=data_tbl[[tops[1]]]
    label <- tops[1]
  } else {
    tops <- c(comp_tbl[[row,1]], comp_tbl[[row,2]], comp_tbl[[row,3]])
    if (tops[2]=="None"){
      z=data_tbl[[tops[1]]]
      label <- tops[1]
    } else {
      z <- do.call('/',list(data_tbl[[tops[1]]],data_tbl[[tops[2]]]))
      z[is.infinite(z)] <- NA
      label <- paste(tops[1], tops[2], sep = paste("_##","/","##_"))
    }
  }
  y <- tops[3]
  data_tbl$zn <- z
  x <- 'zn'
  my.formula <- x~y
  
  if (color.by != "All samples"){
    color.by <- data_tbl[,color.by]
    colors <- scale_color_brewer(palette="Set1")
  } else {
    colors <- scale_color_manual(values = 'black')
  }
  
  plot <- data_tbl %>% ggplot(aes(x = data_tbl$zn, y = data_tbl[,y], color=color.by))+
    xlab(label)+
    ylab(tops[3])+
    geom_point()+
    colors+
    stat_cor(method = 'spearman', label.y.npc = .95)+
    geom_smooth(method=lm, se=F)
  
  return(plot)
}

#Scaterplot and heatmap ##BMI

#Try each phenotype of the disease: phe = c(6:12,14,15)
phe = c(5) #BMI
#phe = c(6) #TRIG
# phe = c(7) #HDL
# phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:87) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.44927536231884 %"
## [1] "2.89855072463768 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.34782608695652 %"
## [1] "5.79710144927536 %"
## [1] "7.2463768115942 %"
## [1] "8.69565217391304 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.1449275362319 %"
## [1] "11.5942028985507 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "13.0434782608696 %"
## [1] "14.4927536231884 %"
## [1] "15.9420289855072 %"
## [1] "17.3913043478261 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.8405797101449 %"
## [1] "20.2898550724638 %"
## [1] "21.7391304347826 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.1884057971014 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "24.6376811594203 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.0869565217391 %"
## [1] "27.536231884058 %"
## [1] "28.9855072463768 %"
## [1] "30.4347826086957 %"
## [1] "31.8840579710145 %"
## [1] "33.3333333333333 %"
## [1] "34.7826086956522 %"
## [1] "36.231884057971 %"
## [1] "37.6811594202899 %"
## [1] "39.1304347826087 %"
## [1] "40.5797101449275 %"
## [1] "42.0289855072464 %"
## [1] "43.4782608695652 %"
## [1] "44.9275362318841 %"
## [1] "46.3768115942029 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.8260869565217 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.2753623188406 %"
## [1] "50.7246376811594 %"
## [1] "52.1739130434783 %"
## [1] "53.6231884057971 %"
## [1] "55.0724637681159 %"
## [1] "56.5217391304348 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.9710144927536 %"
## [1] "59.4202898550725 %"
## [1] "60.8695652173913 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.3188405797101 %"
## [1] "63.768115942029 %"
## [1] "65.2173913043478 %"
## [1] "66.6666666666667 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.1159420289855 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.5652173913043 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "71.0144927536232 %"
## [1] "72.463768115942 %"
## [1] "73.9130434782609 %"
## [1] "75.3623188405797 %"
## [1] "76.8115942028985 %"
## [1] "78.2608695652174 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.7101449275362 %"
## [1] "81.1594202898551 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "82.6086956521739 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "84.0579710144928 %"
## [1] "85.5072463768116 %"
## [1] "86.9565217391304 %"
## [1] "88.4057971014493 %"
## [1] "89.8550724637681 %"
## [1] "91.304347826087 %"
## [1] "92.7536231884058 %"
## [1] "94.2028985507246 %"
## [1] "95.6521739130435 %"
## [1] "97.1014492753623 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "98.5507246376812 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

taxa = c(20:91) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.36986301369863 %"
## [1] "2.73972602739726 %"
## [1] "4.10958904109589 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "5.47945205479452 %"
## [1] "6.84931506849315 %"
## [1] "8.21917808219178 %"
## [1] "9.58904109589041 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.958904109589 %"
## [1] "12.3287671232877 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "13.6986301369863 %"
## [1] "15.0684931506849 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "16.4383561643836 %"
## [1] "17.8082191780822 %"
## [1] "19.1780821917808 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "20.5479452054795 %"
## [1] "21.9178082191781 %"
## [1] "23.2876712328767 %"
## [1] "24.6575342465753 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.027397260274 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "27.3972602739726 %"
## [1] "28.7671232876712 %"
## [1] "30.1369863013699 %"
## [1] "31.5068493150685 %"
## [1] "32.8767123287671 %"
## [1] "34.2465753424658 %"
## [1] "35.6164383561644 %"
## [1] "36.986301369863 %"
## [1] "38.3561643835616 %"
## [1] "39.7260273972603 %"
## [1] "41.0958904109589 %"
## [1] "42.4657534246575 %"
## [1] "43.8356164383562 %"
## [1] "45.2054794520548 %"
## [1] "46.5753424657534 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.945205479452 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.3150684931507 %"
## [1] "50.6849315068493 %"
## [1] "52.0547945205479 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.4246575342466 %"
## [1] "54.7945205479452 %"
## [1] "56.1643835616438 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.5342465753425 %"
## [1] "58.9041095890411 %"
## [1] "60.2739726027397 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.6438356164384 %"
## [1] "63.013698630137 %"
## [1] "64.3835616438356 %"
## [1] "65.7534246575342 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "67.1232876712329 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.4931506849315 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.8630136986301 %"
## [1] "71.2328767123288 %"
## [1] "72.6027397260274 %"
## [1] "73.972602739726 %"
## [1] "75.3424657534247 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.7123287671233 %"
## [1] "78.0821917808219 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.4520547945205 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80.8219178082192 %"
## [1] "82.1917808219178 %"
## [1] "83.5616438356164 %"
## [1] "84.9315068493151 %"
## [1] "86.3013698630137 %"
## [1] "87.6712328767123 %"
## [1] "89.041095890411 %"
## [1] "90.4109589041096 %"
## [1] "91.7808219178082 %"
## [1] "93.1506849315068 %"
## [1] "94.5205479452055 %"
## [1] "95.8904109589041 %"
## [1] "97.2602739726027 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "98.6301369863014 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 2 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 2 rows containing non-finite values (stat_smooth).
## Warning: Removed 2 rows containing missing values (geom_point).

##TRIG

phe = c(6) #TRIG
# phe = c(7) #HDL
# phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:87) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.44927536231884 %"
## [1] "2.89855072463768 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.34782608695652 %"
## [1] "5.79710144927536 %"
## [1] "7.2463768115942 %"
## [1] "8.69565217391304 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.1449275362319 %"
## [1] "11.5942028985507 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "13.0434782608696 %"
## [1] "14.4927536231884 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.9420289855072 %"
## [1] "17.3913043478261 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.8405797101449 %"
## [1] "20.2898550724638 %"
## [1] "21.7391304347826 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.1884057971014 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "24.6376811594203 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.0869565217391 %"
## [1] "27.536231884058 %"
## [1] "28.9855072463768 %"
## [1] "30.4347826086957 %"
## [1] "31.8840579710145 %"
## [1] "33.3333333333333 %"
## [1] "34.7826086956522 %"
## [1] "36.231884057971 %"
## [1] "37.6811594202899 %"
## [1] "39.1304347826087 %"
## [1] "40.5797101449275 %"
## [1] "42.0289855072464 %"
## [1] "43.4782608695652 %"
## [1] "44.9275362318841 %"
## [1] "46.3768115942029 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.8260869565217 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.2753623188406 %"
## [1] "50.7246376811594 %"
## [1] "52.1739130434783 %"
## [1] "53.6231884057971 %"
## [1] "55.0724637681159 %"
## [1] "56.5217391304348 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.9710144927536 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "59.4202898550725 %"
## [1] "60.8695652173913 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.3188405797101 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.768115942029 %"
## [1] "65.2173913043478 %"
## [1] "66.6666666666667 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.1159420289855 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.5652173913043 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "71.0144927536232 %"
## [1] "72.463768115942 %"
## [1] "73.9130434782609 %"
## [1] "75.3623188405797 %"
## [1] "76.8115942028985 %"
## [1] "78.2608695652174 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.7101449275362 %"
## [1] "81.1594202898551 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "82.6086956521739 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "84.0579710144928 %"
## [1] "85.5072463768116 %"
## [1] "86.9565217391304 %"
## [1] "88.4057971014493 %"
## [1] "89.8550724637681 %"
## [1] "91.304347826087 %"
## [1] "92.7536231884058 %"
## [1] "94.2028985507246 %"
## [1] "95.6521739130435 %"
## [1] "97.1014492753623 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "98.5507246376812 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 73 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 73 rows containing non-finite values (stat_smooth).
## Warning: Removed 73 rows containing missing values (geom_point).

taxa = c(20:91) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.36986301369863 %"
## [1] "2.73972602739726 %"
## [1] "4.10958904109589 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "5.47945205479452 %"
## [1] "6.84931506849315 %"
## [1] "8.21917808219178 %"
## [1] "9.58904109589041 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.958904109589 %"
## [1] "12.3287671232877 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "13.6986301369863 %"
## [1] "15.0684931506849 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "16.4383561643836 %"
## [1] "17.8082191780822 %"
## [1] "19.1780821917808 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "20.5479452054795 %"
## [1] "21.9178082191781 %"
## [1] "23.2876712328767 %"
## [1] "24.6575342465753 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.027397260274 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "27.3972602739726 %"
## [1] "28.7671232876712 %"
## [1] "30.1369863013699 %"
## [1] "31.5068493150685 %"
## [1] "32.8767123287671 %"
## [1] "34.2465753424658 %"
## [1] "35.6164383561644 %"
## [1] "36.986301369863 %"
## [1] "38.3561643835616 %"
## [1] "39.7260273972603 %"
## [1] "41.0958904109589 %"
## [1] "42.4657534246575 %"
## [1] "43.8356164383562 %"
## [1] "45.2054794520548 %"
## [1] "46.5753424657534 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.945205479452 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.3150684931507 %"
## [1] "50.6849315068493 %"
## [1] "52.0547945205479 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.4246575342466 %"
## [1] "54.7945205479452 %"
## [1] "56.1643835616438 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.5342465753425 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "58.9041095890411 %"
## [1] "60.2739726027397 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.6438356164384 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.013698630137 %"
## [1] "64.3835616438356 %"
## [1] "65.7534246575342 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "67.1232876712329 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.4931506849315 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.8630136986301 %"
## [1] "71.2328767123288 %"
## [1] "72.6027397260274 %"
## [1] "73.972602739726 %"
## [1] "75.3424657534247 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.7123287671233 %"
## [1] "78.0821917808219 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.4520547945205 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80.8219178082192 %"
## [1] "82.1917808219178 %"
## [1] "83.5616438356164 %"
## [1] "84.9315068493151 %"
## [1] "86.3013698630137 %"
## [1] "87.6712328767123 %"
## [1] "89.041095890411 %"
## [1] "90.4109589041096 %"
## [1] "91.7808219178082 %"
## [1] "93.1506849315068 %"
## [1] "94.5205479452055 %"
## [1] "95.8904109589041 %"
## [1] "97.2602739726027 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "98.6301369863014 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 88 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 88 rows containing non-finite values (stat_smooth).
## Warning: Removed 88 rows containing missing values (geom_point).

##HDL

phe = c(7) #HDL
# phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:87) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.44927536231884 %"
## [1] "2.89855072463768 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.34782608695652 %"
## [1] "5.79710144927536 %"
## [1] "7.2463768115942 %"
## [1] "8.69565217391304 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.1449275362319 %"
## [1] "11.5942028985507 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "13.0434782608696 %"
## [1] "14.4927536231884 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.9420289855072 %"
## [1] "17.3913043478261 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.8405797101449 %"
## [1] "20.2898550724638 %"
## [1] "21.7391304347826 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.1884057971014 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "24.6376811594203 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.0869565217391 %"
## [1] "27.536231884058 %"
## [1] "28.9855072463768 %"
## [1] "30.4347826086957 %"
## [1] "31.8840579710145 %"
## [1] "33.3333333333333 %"
## [1] "34.7826086956522 %"
## [1] "36.231884057971 %"
## [1] "37.6811594202899 %"
## [1] "39.1304347826087 %"
## [1] "40.5797101449275 %"
## [1] "42.0289855072464 %"
## [1] "43.4782608695652 %"
## [1] "44.9275362318841 %"
## [1] "46.3768115942029 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.8260869565217 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.2753623188406 %"
## [1] "50.7246376811594 %"
## [1] "52.1739130434783 %"
## [1] "53.6231884057971 %"
## [1] "55.0724637681159 %"
## [1] "56.5217391304348 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.9710144927536 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "59.4202898550725 %"
## [1] "60.8695652173913 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.3188405797101 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.768115942029 %"
## [1] "65.2173913043478 %"
## [1] "66.6666666666667 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.1159420289855 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.5652173913043 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "71.0144927536232 %"
## [1] "72.463768115942 %"
## [1] "73.9130434782609 %"
## [1] "75.3623188405797 %"
## [1] "76.8115942028985 %"
## [1] "78.2608695652174 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.7101449275362 %"
## [1] "81.1594202898551 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "82.6086956521739 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "84.0579710144928 %"
## [1] "85.5072463768116 %"
## [1] "86.9565217391304 %"
## [1] "88.4057971014493 %"
## [1] "89.8550724637681 %"
## [1] "91.304347826087 %"
## [1] "92.7536231884058 %"
## [1] "94.2028985507246 %"
## [1] "95.6521739130435 %"
## [1] "97.1014492753623 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "98.5507246376812 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 74 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 74 rows containing non-finite values (stat_smooth).
## Warning: Removed 74 rows containing missing values (geom_point).

taxa = c(20:91) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.36986301369863 %"
## [1] "2.73972602739726 %"
## [1] "4.10958904109589 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "5.47945205479452 %"
## [1] "6.84931506849315 %"
## [1] "8.21917808219178 %"
## [1] "9.58904109589041 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.958904109589 %"
## [1] "12.3287671232877 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "13.6986301369863 %"
## [1] "15.0684931506849 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "16.4383561643836 %"
## [1] "17.8082191780822 %"
## [1] "19.1780821917808 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "20.5479452054795 %"
## [1] "21.9178082191781 %"
## [1] "23.2876712328767 %"
## [1] "24.6575342465753 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.027397260274 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "27.3972602739726 %"
## [1] "28.7671232876712 %"
## [1] "30.1369863013699 %"
## [1] "31.5068493150685 %"
## [1] "32.8767123287671 %"
## [1] "34.2465753424658 %"
## [1] "35.6164383561644 %"
## [1] "36.986301369863 %"
## [1] "38.3561643835616 %"
## [1] "39.7260273972603 %"
## [1] "41.0958904109589 %"
## [1] "42.4657534246575 %"
## [1] "43.8356164383562 %"
## [1] "45.2054794520548 %"
## [1] "46.5753424657534 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.945205479452 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.3150684931507 %"
## [1] "50.6849315068493 %"
## [1] "52.0547945205479 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.4246575342466 %"
## [1] "54.7945205479452 %"
## [1] "56.1643835616438 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.5342465753425 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "58.9041095890411 %"
## [1] "60.2739726027397 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.6438356164384 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.013698630137 %"
## [1] "64.3835616438356 %"
## [1] "65.7534246575342 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "67.1232876712329 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.4931506849315 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.8630136986301 %"
## [1] "71.2328767123288 %"
## [1] "72.6027397260274 %"
## [1] "73.972602739726 %"
## [1] "75.3424657534247 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.7123287671233 %"
## [1] "78.0821917808219 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.4520547945205 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80.8219178082192 %"
## [1] "82.1917808219178 %"
## [1] "83.5616438356164 %"
## [1] "84.9315068493151 %"
## [1] "86.3013698630137 %"
## [1] "87.6712328767123 %"
## [1] "89.041095890411 %"
## [1] "90.4109589041096 %"
## [1] "91.7808219178082 %"
## [1] "93.1506849315068 %"
## [1] "94.5205479452055 %"
## [1] "95.8904109589041 %"
## [1] "97.2602739726027 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "98.6301369863014 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 90 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 90 rows containing non-finite values (stat_smooth).
## Warning: Removed 90 rows containing missing values (geom_point).

##Systolic

phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:87) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.44927536231884 %"
## [1] "2.89855072463768 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.34782608695652 %"
## [1] "5.79710144927536 %"
## [1] "7.2463768115942 %"
## [1] "8.69565217391304 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.1449275362319 %"
## [1] "11.5942028985507 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "13.0434782608696 %"
## [1] "14.4927536231884 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.9420289855072 %"
## [1] "17.3913043478261 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.8405797101449 %"
## [1] "20.2898550724638 %"
## [1] "21.7391304347826 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.1884057971014 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "24.6376811594203 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.0869565217391 %"
## [1] "27.536231884058 %"
## [1] "28.9855072463768 %"
## [1] "30.4347826086957 %"
## [1] "31.8840579710145 %"
## [1] "33.3333333333333 %"
## [1] "34.7826086956522 %"
## [1] "36.231884057971 %"
## [1] "37.6811594202899 %"
## [1] "39.1304347826087 %"
## [1] "40.5797101449275 %"
## [1] "42.0289855072464 %"
## [1] "43.4782608695652 %"
## [1] "44.9275362318841 %"
## [1] "46.3768115942029 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.8260869565217 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.2753623188406 %"
## [1] "50.7246376811594 %"
## [1] "52.1739130434783 %"
## [1] "53.6231884057971 %"
## [1] "55.0724637681159 %"
## [1] "56.5217391304348 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.9710144927536 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "59.4202898550725 %"
## [1] "60.8695652173913 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.3188405797101 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.768115942029 %"
## [1] "65.2173913043478 %"
## [1] "66.6666666666667 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.1159420289855 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.5652173913043 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "71.0144927536232 %"
## [1] "72.463768115942 %"
## [1] "73.9130434782609 %"
## [1] "75.3623188405797 %"
## [1] "76.8115942028985 %"
## [1] "78.2608695652174 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.7101449275362 %"
## [1] "81.1594202898551 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "82.6086956521739 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "84.0579710144928 %"
## [1] "85.5072463768116 %"
## [1] "86.9565217391304 %"
## [1] "88.4057971014493 %"
## [1] "89.8550724637681 %"
## [1] "91.304347826087 %"
## [1] "92.7536231884058 %"
## [1] "94.2028985507246 %"
## [1] "95.6521739130435 %"
## [1] "97.1014492753623 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "98.5507246376812 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

taxa = c(20:91) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.36986301369863 %"
## [1] "2.73972602739726 %"
## [1] "4.10958904109589 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "5.47945205479452 %"
## [1] "6.84931506849315 %"
## [1] "8.21917808219178 %"
## [1] "9.58904109589041 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.958904109589 %"
## [1] "12.3287671232877 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "13.6986301369863 %"
## [1] "15.0684931506849 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "16.4383561643836 %"
## [1] "17.8082191780822 %"
## [1] "19.1780821917808 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "20.5479452054795 %"
## [1] "21.9178082191781 %"
## [1] "23.2876712328767 %"
## [1] "24.6575342465753 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.027397260274 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "27.3972602739726 %"
## [1] "28.7671232876712 %"
## [1] "30.1369863013699 %"
## [1] "31.5068493150685 %"
## [1] "32.8767123287671 %"
## [1] "34.2465753424658 %"
## [1] "35.6164383561644 %"
## [1] "36.986301369863 %"
## [1] "38.3561643835616 %"
## [1] "39.7260273972603 %"
## [1] "41.0958904109589 %"
## [1] "42.4657534246575 %"
## [1] "43.8356164383562 %"
## [1] "45.2054794520548 %"
## [1] "46.5753424657534 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.945205479452 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.3150684931507 %"
## [1] "50.6849315068493 %"
## [1] "52.0547945205479 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.4246575342466 %"
## [1] "54.7945205479452 %"
## [1] "56.1643835616438 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.5342465753425 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "58.9041095890411 %"
## [1] "60.2739726027397 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.6438356164384 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.013698630137 %"
## [1] "64.3835616438356 %"
## [1] "65.7534246575342 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "67.1232876712329 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.4931506849315 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.8630136986301 %"
## [1] "71.2328767123288 %"
## [1] "72.6027397260274 %"
## [1] "73.972602739726 %"
## [1] "75.3424657534247 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.7123287671233 %"
## [1] "78.0821917808219 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.4520547945205 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80.8219178082192 %"
## [1] "82.1917808219178 %"
## [1] "83.5616438356164 %"
## [1] "84.9315068493151 %"
## [1] "86.3013698630137 %"
## [1] "87.6712328767123 %"
## [1] "89.041095890411 %"
## [1] "90.4109589041096 %"
## [1] "91.7808219178082 %"
## [1] "93.1506849315068 %"
## [1] "94.5205479452055 %"
## [1] "95.8904109589041 %"
## [1] "97.2602739726027 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "98.6301369863014 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

##Diastolic

phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:87) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.44927536231884 %"
## [1] "2.89855072463768 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.34782608695652 %"
## [1] "5.79710144927536 %"
## [1] "7.2463768115942 %"
## [1] "8.69565217391304 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.1449275362319 %"
## [1] "11.5942028985507 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "13.0434782608696 %"
## [1] "14.4927536231884 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.9420289855072 %"
## [1] "17.3913043478261 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.8405797101449 %"
## [1] "20.2898550724638 %"
## [1] "21.7391304347826 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.1884057971014 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "24.6376811594203 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.0869565217391 %"
## [1] "27.536231884058 %"
## [1] "28.9855072463768 %"
## [1] "30.4347826086957 %"
## [1] "31.8840579710145 %"
## [1] "33.3333333333333 %"
## [1] "34.7826086956522 %"
## [1] "36.231884057971 %"
## [1] "37.6811594202899 %"
## [1] "39.1304347826087 %"
## [1] "40.5797101449275 %"
## [1] "42.0289855072464 %"
## [1] "43.4782608695652 %"
## [1] "44.9275362318841 %"
## [1] "46.3768115942029 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.8260869565217 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.2753623188406 %"
## [1] "50.7246376811594 %"
## [1] "52.1739130434783 %"
## [1] "53.6231884057971 %"
## [1] "55.0724637681159 %"
## [1] "56.5217391304348 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.9710144927536 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "59.4202898550725 %"
## [1] "60.8695652173913 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.3188405797101 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.768115942029 %"
## [1] "65.2173913043478 %"
## [1] "66.6666666666667 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.1159420289855 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.5652173913043 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "71.0144927536232 %"
## [1] "72.463768115942 %"
## [1] "73.9130434782609 %"
## [1] "75.3623188405797 %"
## [1] "76.8115942028985 %"
## [1] "78.2608695652174 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.7101449275362 %"
## [1] "81.1594202898551 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "82.6086956521739 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "84.0579710144928 %"
## [1] "85.5072463768116 %"
## [1] "86.9565217391304 %"
## [1] "88.4057971014493 %"
## [1] "89.8550724637681 %"
## [1] "91.304347826087 %"
## [1] "92.7536231884058 %"
## [1] "94.2028985507246 %"
## [1] "95.6521739130435 %"
## [1] "97.1014492753623 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "98.5507246376812 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

taxa = c(20:91) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.36986301369863 %"
## [1] "2.73972602739726 %"
## [1] "4.10958904109589 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "5.47945205479452 %"
## [1] "6.84931506849315 %"
## [1] "8.21917808219178 %"
## [1] "9.58904109589041 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.958904109589 %"
## [1] "12.3287671232877 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "13.6986301369863 %"
## [1] "15.0684931506849 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "16.4383561643836 %"
## [1] "17.8082191780822 %"
## [1] "19.1780821917808 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "20.5479452054795 %"
## [1] "21.9178082191781 %"
## [1] "23.2876712328767 %"
## [1] "24.6575342465753 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.027397260274 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "27.3972602739726 %"
## [1] "28.7671232876712 %"
## [1] "30.1369863013699 %"
## [1] "31.5068493150685 %"
## [1] "32.8767123287671 %"
## [1] "34.2465753424658 %"
## [1] "35.6164383561644 %"
## [1] "36.986301369863 %"
## [1] "38.3561643835616 %"
## [1] "39.7260273972603 %"
## [1] "41.0958904109589 %"
## [1] "42.4657534246575 %"
## [1] "43.8356164383562 %"
## [1] "45.2054794520548 %"
## [1] "46.5753424657534 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.945205479452 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.3150684931507 %"
## [1] "50.6849315068493 %"
## [1] "52.0547945205479 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.4246575342466 %"
## [1] "54.7945205479452 %"
## [1] "56.1643835616438 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.5342465753425 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "58.9041095890411 %"
## [1] "60.2739726027397 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.6438356164384 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.013698630137 %"
## [1] "64.3835616438356 %"
## [1] "65.7534246575342 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "67.1232876712329 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.4931506849315 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.8630136986301 %"
## [1] "71.2328767123288 %"
## [1] "72.6027397260274 %"
## [1] "73.972602739726 %"
## [1] "75.3424657534247 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.7123287671233 %"
## [1] "78.0821917808219 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.4520547945205 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80.8219178082192 %"
## [1] "82.1917808219178 %"
## [1] "83.5616438356164 %"
## [1] "84.9315068493151 %"
## [1] "86.3013698630137 %"
## [1] "87.6712328767123 %"
## [1] "89.041095890411 %"
## [1] "90.4109589041096 %"
## [1] "91.7808219178082 %"
## [1] "93.1506849315068 %"
## [1] "94.5205479452055 %"
## [1] "95.8904109589041 %"
## [1] "97.2602739726027 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "98.6301369863014 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

##GLU

phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:87) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.44927536231884 %"
## [1] "2.89855072463768 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.34782608695652 %"
## [1] "5.79710144927536 %"
## [1] "7.2463768115942 %"
## [1] "8.69565217391304 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.1449275362319 %"
## [1] "11.5942028985507 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "13.0434782608696 %"
## [1] "14.4927536231884 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.9420289855072 %"
## [1] "17.3913043478261 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.8405797101449 %"
## [1] "20.2898550724638 %"
## [1] "21.7391304347826 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.1884057971014 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "24.6376811594203 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.0869565217391 %"
## [1] "27.536231884058 %"
## [1] "28.9855072463768 %"
## [1] "30.4347826086957 %"
## [1] "31.8840579710145 %"
## [1] "33.3333333333333 %"
## [1] "34.7826086956522 %"
## [1] "36.231884057971 %"
## [1] "37.6811594202899 %"
## [1] "39.1304347826087 %"
## [1] "40.5797101449275 %"
## [1] "42.0289855072464 %"
## [1] "43.4782608695652 %"
## [1] "44.9275362318841 %"
## [1] "46.3768115942029 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.8260869565217 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.2753623188406 %"
## [1] "50.7246376811594 %"
## [1] "52.1739130434783 %"
## [1] "53.6231884057971 %"
## [1] "55.0724637681159 %"
## [1] "56.5217391304348 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.9710144927536 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "59.4202898550725 %"
## [1] "60.8695652173913 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.3188405797101 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.768115942029 %"
## [1] "65.2173913043478 %"
## [1] "66.6666666666667 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.1159420289855 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.5652173913043 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "71.0144927536232 %"
## [1] "72.463768115942 %"
## [1] "73.9130434782609 %"
## [1] "75.3623188405797 %"
## [1] "76.8115942028985 %"
## [1] "78.2608695652174 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.7101449275362 %"
## [1] "81.1594202898551 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "82.6086956521739 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "84.0579710144928 %"
## [1] "85.5072463768116 %"
## [1] "86.9565217391304 %"
## [1] "88.4057971014493 %"
## [1] "89.8550724637681 %"
## [1] "91.304347826087 %"
## [1] "92.7536231884058 %"
## [1] "94.2028985507246 %"
## [1] "95.6521739130435 %"
## [1] "97.1014492753623 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "98.5507246376812 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 74 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 74 rows containing non-finite values (stat_smooth).
## Warning: Removed 74 rows containing missing values (geom_point).

taxa = c(20:91) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.36986301369863 %"
## [1] "2.73972602739726 %"
## [1] "4.10958904109589 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "5.47945205479452 %"
## [1] "6.84931506849315 %"
## [1] "8.21917808219178 %"
## [1] "9.58904109589041 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.958904109589 %"
## [1] "12.3287671232877 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "13.6986301369863 %"
## [1] "15.0684931506849 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "16.4383561643836 %"
## [1] "17.8082191780822 %"
## [1] "19.1780821917808 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "20.5479452054795 %"
## [1] "21.9178082191781 %"
## [1] "23.2876712328767 %"
## [1] "24.6575342465753 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.027397260274 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "27.3972602739726 %"
## [1] "28.7671232876712 %"
## [1] "30.1369863013699 %"
## [1] "31.5068493150685 %"
## [1] "32.8767123287671 %"
## [1] "34.2465753424658 %"
## [1] "35.6164383561644 %"
## [1] "36.986301369863 %"
## [1] "38.3561643835616 %"
## [1] "39.7260273972603 %"
## [1] "41.0958904109589 %"
## [1] "42.4657534246575 %"
## [1] "43.8356164383562 %"
## [1] "45.2054794520548 %"
## [1] "46.5753424657534 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.945205479452 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.3150684931507 %"
## [1] "50.6849315068493 %"
## [1] "52.0547945205479 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.4246575342466 %"
## [1] "54.7945205479452 %"
## [1] "56.1643835616438 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.5342465753425 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "58.9041095890411 %"
## [1] "60.2739726027397 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.6438356164384 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.013698630137 %"
## [1] "64.3835616438356 %"
## [1] "65.7534246575342 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "67.1232876712329 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.4931506849315 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.8630136986301 %"
## [1] "71.2328767123288 %"
## [1] "72.6027397260274 %"
## [1] "73.972602739726 %"
## [1] "75.3424657534247 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.7123287671233 %"
## [1] "78.0821917808219 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.4520547945205 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80.8219178082192 %"
## [1] "82.1917808219178 %"
## [1] "83.5616438356164 %"
## [1] "84.9315068493151 %"
## [1] "86.3013698630137 %"
## [1] "87.6712328767123 %"
## [1] "89.041095890411 %"
## [1] "90.4109589041096 %"
## [1] "91.7808219178082 %"
## [1] "93.1506849315068 %"
## [1] "94.5205479452055 %"
## [1] "95.8904109589041 %"
## [1] "97.2602739726027 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "98.6301369863014 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 90 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 90 rows containing non-finite values (stat_smooth).
## Warning: Removed 90 rows containing missing values (geom_point).

##GH

phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:87) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.44927536231884 %"
## [1] "2.89855072463768 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.34782608695652 %"
## [1] "5.79710144927536 %"
## [1] "7.2463768115942 %"
## [1] "8.69565217391304 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.1449275362319 %"
## [1] "11.5942028985507 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "13.0434782608696 %"
## [1] "14.4927536231884 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.9420289855072 %"
## [1] "17.3913043478261 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.8405797101449 %"
## [1] "20.2898550724638 %"
## [1] "21.7391304347826 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.1884057971014 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "24.6376811594203 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.0869565217391 %"
## [1] "27.536231884058 %"
## [1] "28.9855072463768 %"
## [1] "30.4347826086957 %"
## [1] "31.8840579710145 %"
## [1] "33.3333333333333 %"
## [1] "34.7826086956522 %"
## [1] "36.231884057971 %"
## [1] "37.6811594202899 %"
## [1] "39.1304347826087 %"
## [1] "40.5797101449275 %"
## [1] "42.0289855072464 %"
## [1] "43.4782608695652 %"
## [1] "44.9275362318841 %"
## [1] "46.3768115942029 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.8260869565217 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.2753623188406 %"
## [1] "50.7246376811594 %"
## [1] "52.1739130434783 %"
## [1] "53.6231884057971 %"
## [1] "55.0724637681159 %"
## [1] "56.5217391304348 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.9710144927536 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "59.4202898550725 %"
## [1] "60.8695652173913 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.3188405797101 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.768115942029 %"
## [1] "65.2173913043478 %"
## [1] "66.6666666666667 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.1159420289855 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.5652173913043 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "71.0144927536232 %"
## [1] "72.463768115942 %"
## [1] "73.9130434782609 %"
## [1] "75.3623188405797 %"
## [1] "76.8115942028985 %"
## [1] "78.2608695652174 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.7101449275362 %"
## [1] "81.1594202898551 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "82.6086956521739 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "84.0579710144928 %"
## [1] "85.5072463768116 %"
## [1] "86.9565217391304 %"
## [1] "88.4057971014493 %"
## [1] "89.8550724637681 %"
## [1] "91.304347826087 %"
## [1] "92.7536231884058 %"
## [1] "94.2028985507246 %"
## [1] "95.6521739130435 %"
## [1] "97.1014492753623 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "98.5507246376812 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 74 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 74 rows containing non-finite values (stat_smooth).
## Warning: Removed 74 rows containing missing values (geom_point).

taxa = c(20:91) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.36986301369863 %"
## [1] "2.73972602739726 %"
## [1] "4.10958904109589 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "5.47945205479452 %"
## [1] "6.84931506849315 %"
## [1] "8.21917808219178 %"
## [1] "9.58904109589041 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.958904109589 %"
## [1] "12.3287671232877 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "13.6986301369863 %"
## [1] "15.0684931506849 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "16.4383561643836 %"
## [1] "17.8082191780822 %"
## [1] "19.1780821917808 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "20.5479452054795 %"
## [1] "21.9178082191781 %"
## [1] "23.2876712328767 %"
## [1] "24.6575342465753 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.027397260274 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "27.3972602739726 %"
## [1] "28.7671232876712 %"
## [1] "30.1369863013699 %"
## [1] "31.5068493150685 %"
## [1] "32.8767123287671 %"
## [1] "34.2465753424658 %"
## [1] "35.6164383561644 %"
## [1] "36.986301369863 %"
## [1] "38.3561643835616 %"
## [1] "39.7260273972603 %"
## [1] "41.0958904109589 %"
## [1] "42.4657534246575 %"
## [1] "43.8356164383562 %"
## [1] "45.2054794520548 %"
## [1] "46.5753424657534 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.945205479452 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.3150684931507 %"
## [1] "50.6849315068493 %"
## [1] "52.0547945205479 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.4246575342466 %"
## [1] "54.7945205479452 %"
## [1] "56.1643835616438 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.5342465753425 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "58.9041095890411 %"
## [1] "60.2739726027397 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.6438356164384 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.013698630137 %"
## [1] "64.3835616438356 %"
## [1] "65.7534246575342 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "67.1232876712329 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.4931506849315 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.8630136986301 %"
## [1] "71.2328767123288 %"
## [1] "72.6027397260274 %"
## [1] "73.972602739726 %"
## [1] "75.3424657534247 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.7123287671233 %"
## [1] "78.0821917808219 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.4520547945205 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80.8219178082192 %"
## [1] "82.1917808219178 %"
## [1] "83.5616438356164 %"
## [1] "84.9315068493151 %"
## [1] "86.3013698630137 %"
## [1] "87.6712328767123 %"
## [1] "89.041095890411 %"
## [1] "90.4109589041096 %"
## [1] "91.7808219178082 %"
## [1] "93.1506849315068 %"
## [1] "94.5205479452055 %"
## [1] "95.8904109589041 %"
## [1] "97.2602739726027 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "98.6301369863014 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 90 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 90 rows containing non-finite values (stat_smooth).
## Warning: Removed 90 rows containing missing values (geom_point).

##AGE

phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:87) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.44927536231884 %"
## [1] "2.89855072463768 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.34782608695652 %"
## [1] "5.79710144927536 %"
## [1] "7.2463768115942 %"
## [1] "8.69565217391304 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.1449275362319 %"
## [1] "11.5942028985507 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "13.0434782608696 %"
## [1] "14.4927536231884 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.9420289855072 %"
## [1] "17.3913043478261 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.8405797101449 %"
## [1] "20.2898550724638 %"
## [1] "21.7391304347826 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.1884057971014 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "24.6376811594203 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.0869565217391 %"
## [1] "27.536231884058 %"
## [1] "28.9855072463768 %"
## [1] "30.4347826086957 %"
## [1] "31.8840579710145 %"
## [1] "33.3333333333333 %"
## [1] "34.7826086956522 %"
## [1] "36.231884057971 %"
## [1] "37.6811594202899 %"
## [1] "39.1304347826087 %"
## [1] "40.5797101449275 %"
## [1] "42.0289855072464 %"
## [1] "43.4782608695652 %"
## [1] "44.9275362318841 %"
## [1] "46.3768115942029 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.8260869565217 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.2753623188406 %"
## [1] "50.7246376811594 %"
## [1] "52.1739130434783 %"
## [1] "53.6231884057971 %"
## [1] "55.0724637681159 %"
## [1] "56.5217391304348 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.9710144927536 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "59.4202898550725 %"
## [1] "60.8695652173913 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.3188405797101 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.768115942029 %"
## [1] "65.2173913043478 %"
## [1] "66.6666666666667 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.1159420289855 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.5652173913043 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "71.0144927536232 %"
## [1] "72.463768115942 %"
## [1] "73.9130434782609 %"
## [1] "75.3623188405797 %"
## [1] "76.8115942028985 %"
## [1] "78.2608695652174 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.7101449275362 %"
## [1] "81.1594202898551 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "82.6086956521739 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "84.0579710144928 %"
## [1] "85.5072463768116 %"
## [1] "86.9565217391304 %"
## [1] "88.4057971014493 %"
## [1] "89.8550724637681 %"
## [1] "91.304347826087 %"
## [1] "92.7536231884058 %"
## [1] "94.2028985507246 %"
## [1] "95.6521739130435 %"
## [1] "97.1014492753623 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "98.5507246376812 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

taxa = c(20:91) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.36986301369863 %"
## [1] "2.73972602739726 %"
## [1] "4.10958904109589 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "5.47945205479452 %"
## [1] "6.84931506849315 %"
## [1] "8.21917808219178 %"
## [1] "9.58904109589041 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.958904109589 %"
## [1] "12.3287671232877 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "13.6986301369863 %"
## [1] "15.0684931506849 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "16.4383561643836 %"
## [1] "17.8082191780822 %"
## [1] "19.1780821917808 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "20.5479452054795 %"
## [1] "21.9178082191781 %"
## [1] "23.2876712328767 %"
## [1] "24.6575342465753 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.027397260274 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "27.3972602739726 %"
## [1] "28.7671232876712 %"
## [1] "30.1369863013699 %"
## [1] "31.5068493150685 %"
## [1] "32.8767123287671 %"
## [1] "34.2465753424658 %"
## [1] "35.6164383561644 %"
## [1] "36.986301369863 %"
## [1] "38.3561643835616 %"
## [1] "39.7260273972603 %"
## [1] "41.0958904109589 %"
## [1] "42.4657534246575 %"
## [1] "43.8356164383562 %"
## [1] "45.2054794520548 %"
## [1] "46.5753424657534 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.945205479452 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.3150684931507 %"
## [1] "50.6849315068493 %"
## [1] "52.0547945205479 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.4246575342466 %"
## [1] "54.7945205479452 %"
## [1] "56.1643835616438 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.5342465753425 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "58.9041095890411 %"
## [1] "60.2739726027397 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.6438356164384 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.013698630137 %"
## [1] "64.3835616438356 %"
## [1] "65.7534246575342 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "67.1232876712329 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.4931506849315 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.8630136986301 %"
## [1] "71.2328767123288 %"
## [1] "72.6027397260274 %"
## [1] "73.972602739726 %"
## [1] "75.3424657534247 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.7123287671233 %"
## [1] "78.0821917808219 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.4520547945205 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80.8219178082192 %"
## [1] "82.1917808219178 %"
## [1] "83.5616438356164 %"
## [1] "84.9315068493151 %"
## [1] "86.3013698630137 %"
## [1] "87.6712328767123 %"
## [1] "89.041095890411 %"
## [1] "90.4109589041096 %"
## [1] "91.7808219178082 %"
## [1] "93.1506849315068 %"
## [1] "94.5205479452055 %"
## [1] "95.8904109589041 %"
## [1] "97.2602739726027 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "98.6301369863014 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

##Waist

phe = c(14) #Waist


taxa = c(20:87) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.44927536231884 %"
## [1] "2.89855072463768 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.34782608695652 %"
## [1] "5.79710144927536 %"
## [1] "7.2463768115942 %"
## [1] "8.69565217391304 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.1449275362319 %"
## [1] "11.5942028985507 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "13.0434782608696 %"
## [1] "14.4927536231884 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "15.9420289855072 %"
## [1] "17.3913043478261 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.8405797101449 %"
## [1] "20.2898550724638 %"
## [1] "21.7391304347826 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "23.1884057971014 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "24.6376811594203 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.0869565217391 %"
## [1] "27.536231884058 %"
## [1] "28.9855072463768 %"
## [1] "30.4347826086957 %"
## [1] "31.8840579710145 %"
## [1] "33.3333333333333 %"
## [1] "34.7826086956522 %"
## [1] "36.231884057971 %"
## [1] "37.6811594202899 %"
## [1] "39.1304347826087 %"
## [1] "40.5797101449275 %"
## [1] "42.0289855072464 %"
## [1] "43.4782608695652 %"
## [1] "44.9275362318841 %"
## [1] "46.3768115942029 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.8260869565217 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.2753623188406 %"
## [1] "50.7246376811594 %"
## [1] "52.1739130434783 %"
## [1] "53.6231884057971 %"
## [1] "55.0724637681159 %"
## [1] "56.5217391304348 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.9710144927536 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "59.4202898550725 %"
## [1] "60.8695652173913 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.3188405797101 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.768115942029 %"
## [1] "65.2173913043478 %"
## [1] "66.6666666666667 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.1159420289855 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.5652173913043 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "71.0144927536232 %"
## [1] "72.463768115942 %"
## [1] "73.9130434782609 %"
## [1] "75.3623188405797 %"
## [1] "76.8115942028985 %"
## [1] "78.2608695652174 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.7101449275362 %"
## [1] "81.1594202898551 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "82.6086956521739 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "84.0579710144928 %"
## [1] "85.5072463768116 %"
## [1] "86.9565217391304 %"
## [1] "88.4057971014493 %"
## [1] "89.8550724637681 %"
## [1] "91.304347826087 %"
## [1] "92.7536231884058 %"
## [1] "94.2028985507246 %"
## [1] "95.6521739130435 %"
## [1] "97.1014492753623 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "98.5507246376812 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

taxa = c(20:91) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.36986301369863 %"
## [1] "2.73972602739726 %"
## [1] "4.10958904109589 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "5.47945205479452 %"
## [1] "6.84931506849315 %"
## [1] "8.21917808219178 %"
## [1] "9.58904109589041 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.958904109589 %"
## [1] "12.3287671232877 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "13.6986301369863 %"
## [1] "15.0684931506849 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "16.4383561643836 %"
## [1] "17.8082191780822 %"
## [1] "19.1780821917808 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "20.5479452054795 %"
## [1] "21.9178082191781 %"
## [1] "23.2876712328767 %"
## [1] "24.6575342465753 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.027397260274 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "27.3972602739726 %"
## [1] "28.7671232876712 %"
## [1] "30.1369863013699 %"
## [1] "31.5068493150685 %"
## [1] "32.8767123287671 %"
## [1] "34.2465753424658 %"
## [1] "35.6164383561644 %"
## [1] "36.986301369863 %"
## [1] "38.3561643835616 %"
## [1] "39.7260273972603 %"
## [1] "41.0958904109589 %"
## [1] "42.4657534246575 %"
## [1] "43.8356164383562 %"
## [1] "45.2054794520548 %"
## [1] "46.5753424657534 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "47.945205479452 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.3150684931507 %"
## [1] "50.6849315068493 %"
## [1] "52.0547945205479 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.4246575342466 %"
## [1] "54.7945205479452 %"
## [1] "56.1643835616438 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.5342465753425 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "58.9041095890411 %"
## [1] "60.2739726027397 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.6438356164384 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.013698630137 %"
## [1] "64.3835616438356 %"
## [1] "65.7534246575342 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "67.1232876712329 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.4931506849315 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.8630136986301 %"
## [1] "71.2328767123288 %"
## [1] "72.6027397260274 %"
## [1] "73.972602739726 %"
## [1] "75.3424657534247 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.7123287671233 %"
## [1] "78.0821917808219 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.4520547945205 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "80.8219178082192 %"
## [1] "82.1917808219178 %"
## [1] "83.5616438356164 %"
## [1] "84.9315068493151 %"
## [1] "86.3013698630137 %"
## [1] "87.6712328767123 %"
## [1] "89.041095890411 %"
## [1] "90.4109589041096 %"
## [1] "91.7808219178082 %"
## [1] "93.1506849315068 %"
## [1] "94.5205479452055 %"
## [1] "95.8904109589041 %"
## [1] "97.2602739726027 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "98.6301369863014 %"
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

#Heatmap

#Male
# Visualizing the correlation in heatmap [30x30]; try with class x class- level 3
library(corrplot)
res = cor.mtest(merged.table_male[,c(5:11,13,14,20:87)], conf.level = 0.95, rm.na = T)
## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero
Correlation <- round(cor(merged.table_male[,c(5:11,13,14,20:87)],method = "spearman", use="complete.obs"), 2)
## Warning in cor(merged.table_male[, c(5:11, 13, 14, 20:87)], method =
## "spearman", : the standard deviation is zero
corrplot(Correlation, method = "ellipse", tl.col = "black", type = 'upper', tl.cex = 0.4, cl.cex = 0.4, p.mat = res$p, insig = "blank", sig.level = 0.05) #heatmap; blue=neg corr; red=pos corr

#Female
# Visualizing the correlation in heatmap [30x30]; try with class x class- level 3
library(corrplot)
res = cor.mtest(merged.table_female[,c(5:11,13,14,20:91)], conf.level = 0.95, rm.na = T)
## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero
Correlation <- round(cor(merged.table_female[,c(5:11,13,14,20:91)],method = "spearman", use="complete.obs"), 2)
## Warning in cor(merged.table_female[, c(5:11, 13, 14, 20:91)], method =
## "spearman", : the standard deviation is zero
corrplot(Correlation, method = "ellipse", tl.col = "black", type = 'upper', tl.cex = 0.4, cl.cex = 0.4, p.mat = res$p, insig = "blank", sig.level = 0.05) #heatmap; blue=neg corr; red=pos corr
## Warning in corrplot(Correlation, method = "ellipse", tl.col = "black", type =
## "upper", : Not been able to calculate text margin, please try again with a clean
## new empty window using {plot.new(); dev.off()} or reduce tl.cex

#Read dataframes_level6_genus

#ASVs <- read_qza("microbiome_data/filtered/table_filt.qza") #Gives me an error so I commented out.
taxa_table <- read.csv("level-6_genus_taxtable_clean.csv", header=T) # csv obtained from /Users/giovanna/OneDrive - UW-Madison/Rotations/3 Denu-Rey/SHOW data/microbiome_data/taxa/taxa_barplot.qza
taxa_table = taxa_table[,1:283] #all rows, from columns 1 to 528
taxa_ra <- sweep(taxa_table[,2:ncol(taxa_table)],1,rowSums(taxa_table[,2:ncol(taxa_table)]),"/") #relative abundance - normalization of sample reads
taxa_ra$index = taxa_table$index
merged.table_genus <- merge(MetS_feature, taxa_ra, by.x="16S_ID", by.y="index")

merged.table_male <- merged.table_genus %>%
  filter(GENDER == "[1] Male")
merged.table_female <- merged.table_genus %>%
  filter(GENDER == "[2] Female")

#Regression
MetS_feature$MetS <- ifelse((MetS_feature$MetS.binary == 1) | (MetS_feature$gh.binary ==1), 1, 0)
reg_data_genus <- merged.table_genus %>% select(MetS,AGE_CONSENT, ANT_BMI, PMRC_LAB_TRIG, PMRC_LAB_HDLCHOL, BP_SYSTOLIC_23, BP_DIASTOLIC_23, PMRC_LAB_GLU, PMRC_LAB_GH, ANT_MEAS_WAIST_CM, starts_with("D_0__"))
lmod <- glm(MetS ~ ., family = "binomial", data = reg_data_genus)
## Warning: glm.fit: algorithm did not converge
summary(lmod)
## 
## Call:
## glm(formula = MetS ~ ., family = "binomial", data = reg_data_genus)
## 
## Deviance Residuals: 
##   [1]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
##  [26]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
##  [51]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
##  [76]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
## [101]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
## 
## Coefficients: (171 not defined because of singularities)
##                                                                                                                                                                                              Estimate
## (Intercept)                                                                                                                                                                                -1.344e+03
## AGE_CONSENT                                                                                                                                                                                 2.023e+00
## ANT_BMI                                                                                                                                                                                     2.271e-01
## PMRC_LAB_TRIG                                                                                                                                                                               5.092e-01
## PMRC_LAB_HDLCHOL                                                                                                                                                                            1.102e+01
## BP_SYSTOLIC_23                                                                                                                                                                              6.689e+00
## BP_DIASTOLIC_23                                                                                                                                                                            -1.114e+01
## PMRC_LAB_GLU                                                                                                                                                                               -3.481e-01
## PMRC_LAB_GH                                                                                                                                                                                -6.671e+01
## ANT_MEAS_WAIST_CM                                                                                                                                                                           6.863e+00
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria.D_3__Methanobacteriales.D_4__Methanobacteriaceae.D_5__Methanobrevibacter                                                               6.565e+04
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria.D_3__Methanobacteriales.D_4__Methanobacteriaceae.D_5__Methanosphaera                                                                   1.485e+06
## D_0__Archaea.D_1__Euryarchaeota.D_2__Thermoplasmata.D_3__Methanomassiliicoccales.D_4__Methanomassiliicoccaceae.D_5__Methanomassiliicoccus                                                  -4.642e+06
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales.D_4__Actinomycetaceae.D_5__Actinomyces                                                                           1.766e+06
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales.D_4__Actinomycetaceae.D_5__Mobiluncus                                                                           -7.485e+08
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales.D_4__Actinomycetaceae.D_5__Varibaculum                                                                          -6.721e+06
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Bifidobacteriales.D_4__Bifidobacteriaceae.D_5__Bifidobacterium                                                                  -1.357e+03
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Corynebacteriales.D_4__Corynebacteriaceae.D_5__Lawsonella                                                                       -1.991e+08
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Micrococcales.D_4__Micrococcaceae.D_5__Rothia                                                                                   -2.179e+06
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Atopobiaceae.D_5__Libanicoccus                                                                            -2.760e+05
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Atopobiaceae.D_5__Olsenella                                                                               -8.906e+06
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Coriobacteriaceae.D_5__Collinsella                                                                         2.495e+04
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Coriobacteriales.Incertae.Sedis.D_5__uncultured                                                            1.236e+05
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Adlercreutzia                                                                         9.330e+05
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__CHKCI002                                                                             -8.419e+06
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Eggerthella                                                                          -4.002e+04
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Enterorhabdus                                                                        -1.092e+06
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Gordonibacter                                                                         3.111e+05
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Parvibacter                                                                           1.136e+05
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Senegalimassilia                                                                      8.262e+05
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Slackia                                                                              -3.492e+05
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__uncultured                                                                            3.079e+05
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__uncultured.D_5__uncultured.bacterium                                                                      -1.757e+05
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Bacteroidaceae.D_5__Bacteroides                                                                                   5.217e+02
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Barnesiellaceae.D_5__Barnesiella                                                                                  1.806e+03
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Barnesiellaceae.D_5__Coprobacter                                                                                  8.954e+04
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Barnesiellaceae.D_5__uncultured                                                                                  -3.351e+06
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Dysgonomonadaceae.D_5__Dysgonomonas                                                                              -6.967e+05
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Marinifilaceae.D_5__Butyricimonas                                                                                 4.099e+05
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Marinifilaceae.D_5__Odoribacter                                                                                   3.314e+04
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Marinifilaceae.D_5__Sanguibacteroides                                                                             2.305e+07
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__Muribaculum                                                                                          NA
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__metagenome                                                                                    1.160e+05
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__uncultured.Porphyromonadaceae.bacterium                                                       4.867e+05
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__uncultured.bacterium                                                                          3.051e+04
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__uncultured.organism                                                                           1.856e+05
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.__                                                                                                -3.712e+04
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Porphyromonadaceae.D_5__Porphyromonas                                                                            -1.365e+06
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Alloprevotella                                                                               -1.034e+04
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Paraprevotella                                                                               -2.344e+03
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella                                                                                   -4.916e+06
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella.2                                                                                 -1.665e+04
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella.6                                                                                  2.277e+06
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella.7                                                                                 -9.853e+02
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella.9                                                                                  6.501e+02
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotellaceae.NK3B31.group                                                                   3.464e+06
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotellaceae.UCG.001                                                                       -4.731e+06
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__uncultured                                                                                    9.818e+04
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.__                                                                                                -2.645e+08
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae.D_5__Alistipes                                                                                     -6.964e+02
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae.D_5__Millionella                                                                                    3.617e+08
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae.D_5__Rikenella                                                                                      1.014e+06
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae.D_5__Rikenellaceae.RC9.gut.group                                                                    8.889e+04
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Tannerellaceae.D_5__Parabacteroides                                                                              -6.853e+03
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__uncultured.D_5__gut.metagenome                                                                                    5.108e+06
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__uncultured.D_5__uncultured.bacterium                                                                             -1.008e+06
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.__.__                                                                                                                  5.104e+04
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Flavobacteriales.D_4__Flavobacteriaceae.D_5__uncultured                                                                              3.223e+05
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Sphingobacteriales.D_4__Sphingobacteriaceae.D_5__Sphingobacterium                                                                           NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__Candidatus.Gastranaerophilales.bacterium.Zag_111.D_5__Candidatus.Gastranaerophilales.bacterium.Zag_111         NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__Clostridium.sp..CAG.306.D_5__Clostridium.sp..CAG.306                                                           NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__uncultured.bacterium.D_5__uncultured.bacterium                                                          9.699e+04
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.__.__                                                                                                        1.000e+04
## D_0__Bacteria.D_1__Epsilonbacteraeota.D_2__Campylobacteria.D_3__Campylobacterales.D_4__Campylobacteraceae.D_5__Campylobacter                                                                1.036e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales.D_4__Family.XI.D_5__Gemella                                                                                                      5.139e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales.D_4__Staphylococcaceae.D_5__Staphylococcus                                                                                      -4.323e+06
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Carnobacteriaceae.D_5__Carnobacterium                                                                                 -1.033e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Carnobacteriaceae.D_5__Granulicatella                                                                                 -9.153e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Enterococcaceae.D_5__Enterococcus                                                                                      7.750e+04
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Lactobacillaceae.D_5__Lactobacillus                                                                                   -8.521e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Lactobacillaceae.D_5__Pediococcus                                                                                     -1.134e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Leuconostocaceae.D_5__Leuconostoc                                                                                      2.728e+04
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Leuconostocaceae.D_5__Weissella                                                                                        2.375e+06
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Streptococcaceae.D_5__Lactococcus                                                                                     -1.341e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Streptococcaceae.D_5__Streptococcus                                                                                   -4.927e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae.D_5__Catabacter                                                                                   5.216e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae.D_5__Christensenellaceae.R.7.group                                                               -1.302e+04
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae.D_5__uncultured                                                                                  -5.307e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae.__                                                                                               -3.388e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiaceae.1.D_5__Clostridium.sensu.stricto.1                                                                    -7.043e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiaceae.1.D_5__Clostridium.sensu.stricto.13                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__Clostridiales.bacterium.enrichment.culture.clone.06.1235251.67                    -1.172e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__gut.metagenome                                                                    -1.043e+06
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__metagenome                                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__uncultured.Thermoanaerobacterales.bacterium                                        7.765e+04
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__uncultured.bacterium                                                               1.611e+06
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__uncultured.organism                                                               -8.759e+04
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Defluviitaleaceae.D_5__Defluviitaleaceae.UCG.011                                                                      7.656e+04
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Eubacteriaceae.D_5__Anaerofustis                                                                                     -3.745e+06
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Eubacteriaceae.D_5__Eubacterium                                                                                       7.774e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Anaerococcus                                                                                           6.647e+07
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Ezakiella                                                                                             -2.132e+06
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Finegoldia                                                                                            -1.181e+07
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Parvimonas                                                                                            -2.595e+06
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Peptoniphilus                                                                                          4.456e+06
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__W5053                                                                                                  1.085e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__Family.XIII.AD3011.group                                                                            -2.936e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__Family.XIII.UCG.001                                                                                 -8.012e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__Mogibacterium                                                                                       -6.498e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__.Eubacterium..brachy.group                                                                          -5.882e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__.Eubacterium..nodatum.group                                                                          3.572e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__uncultured                                                                                          -1.127e+06
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.__                                                                                                        2.781e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Acetitomaculum                                                                                  -3.742e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Agathobacter                                                                                     2.712e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Anaerosporobacter                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Anaerostipes                                                                                     2.270e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Blautia                                                                                         -1.135e+02
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Butyrivibrio                                                                                    -1.077e+04
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__CAG.56                                                                                          -1.692e+04
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__CHKCI001                                                                                        -1.170e+06
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Cellulosilyticum                                                                                 6.064e+04
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Coprococcus.1                                                                                   -1.331e+04
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Coprococcus.2                                                                                    8.463e+02
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Coprococcus.3                                                                                    7.596e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Cuneatibacter                                                                                   -5.894e+04
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Dorea                                                                                            3.926e+03
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Eisenbergiella                                                                                   1.875e+05
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Epulopiscium                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Fusicatenibacter                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__GCA.900066575                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__GCA.900066755                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Howardella                                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Hungatella                                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnoclostridium                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospira                                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.FCS020.group                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.ND3007.group                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.NK3A20.group                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.NK4A136.group                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.NK4B4.group                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.001                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.003                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.004                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.008                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.010                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lactonifactor                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Marvinbryantia                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Moryella                                                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Murimonas                                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Oribacterium                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Roseburia                                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Sellimonas                                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Shuttleworthia                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Tyzzerella                                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Tyzzerella.3                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Tyzzerella.4                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__UC5.1.2E3                                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..eligens.group                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..fissicatena.group                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..hallii.group                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..ruminantium.group                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..ventriosum.group                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..xylanophilum.group                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Ruminococcus..gauvreauii.group                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Ruminococcus..gnavus.group                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Ruminococcus..torques.group                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__uncultured                                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.__                                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptococcaceae.D_5__Peptococcus                                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptococcaceae.D_5__uncultured                                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Clostridioides                                                                                    NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Intestinibacter                                                                                   NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Paeniclostridium                                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Peptoclostridium                                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Peptostreptococcus                                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Romboutsia                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Terrisporobacter                                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Acetanaerobacterium                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Anaerofilum                                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Anaerotruncus                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Angelakisella                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Butyricicoccus                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__CAG.352                                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Candidatus.Soleaferrea                                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Caproiciproducens                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__DTU089                                                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Faecalibacterium                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Flavonifractor                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Fournierella                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__GCA.900066225                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Harryflintia                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Hydrogenoanaerobacterium                                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Intestinimonas                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Negativibacillus                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Oscillibacter                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Oscillospira                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Phocea                                                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Pseudoflavonifractor                                                                                    NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium.1                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium.5                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium.6                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium.9                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.NK4A214.group                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.002                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.003                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.004                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.005                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.007                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.008                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.009                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.010                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.013                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.014                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcus.1                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcus.2                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Subdoligranulum                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__UBA1819                                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__.Eubacterium..coprostanoligenes.group                                                                   NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__uncultured                                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.__                                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.__.__                                                                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.__.__.__                                                                                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Candidatus.Stoquefichus                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Catenibacterium                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Coprobacillus                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Dielma                                                                                   NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Erysipelatoclostridium                                                                   NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Erysipelotrichaceae.UCG.003                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Erysipelotrichaceae.UCG.004                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Faecalibaculum                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Faecalicoccus                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Faecalitalea                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Holdemanella                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Holdemania                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Merdibacter                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Solobacterium                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Turicibacter                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__.Clostridium..innocuum.group                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__uncultured                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.__                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Acidaminococcaceae.D_5__Acidaminococcus                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Acidaminococcaceae.D_5__Phascolarctobacterium                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Acidaminococcaceae.D_5__Succiniclasticum                                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Allisonella                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Anaeroglobus                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Anaerovibrio                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Dialister                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Megamonas                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Megasphaera                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Mitsuokella                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Veillonella                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__uncultured                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.__                                                                                                      NA
## D_0__Bacteria.D_1__Firmicutes.__.__.__.__                                                                                                                                                          NA
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia.D_3__Fusobacteriales.D_4__Fusobacteriaceae.D_5__Cetobacterium                                                                                   NA
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia.D_3__Fusobacteriales.D_4__Fusobacteriaceae.D_5__Fusobacterium                                                                                   NA
## D_0__Bacteria.D_1__Lentisphaerae.D_2__Lentisphaeria.D_3__Victivallales.D_4__Victivallaceae.D_5__Victivallis                                                                                        NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured.D_5__Azospirillum.sp..47_25                                                                       NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured.D_5__gut.metagenome                                                                               NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured.D_5__uncultured.bacterium                                                                         NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured.__                                                                                                NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.__.__.__                                                                                                                                NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae.D_5__Bilophila                                                                         NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae.D_5__Desulfovibrio                                                                     NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae.D_5__Mailhella                                                                         NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae.D_5__uncultured                                                                        NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Aeromonadales.D_4__Succinivibrionaceae.D_5__Succinivibrio                                                                          NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae.D_5__Comamonas                                                                         NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae.D_5__Parasutterella                                                                    NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae.D_5__Sutterella                                                                        NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae.__                                                                                     NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae.D_5__Escherichia.Shigella                                                                NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae.D_5__Klebsiella                                                                          NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae.D_5__Proteus                                                                             NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae.__                                                                                       NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pasteurellales.D_4__Pasteurellaceae.D_5__Haemophilus                                                                               NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pseudomonadales.D_4__Pseudomonadaceae.D_5__Pseudomonas                                                                             NA
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales.D_4__Synergistaceae.D_5__Cloacibacillus                                                                                       NA
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales.D_4__Synergistaceae.D_5__Fretibacterium                                                                                       NA
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales.D_4__Synergistaceae.D_5__Pyramidobacter                                                                                       NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales.D_4__gut.metagenome.D_5__gut.metagenome                                                                                       NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales.D_4__uncultured.organism.D_5__uncultured.organism                                                                             NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__Firmicutes.bacterium.CAG.822.D_5__Firmicutes.bacterium.CAG.822                                                            NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__gut.metagenome.D_5__gut.metagenome                                                                                        NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__uncultured.bacterium.adhufec202.D_5__uncultured.bacterium.adhufec202                                                      NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__uncultured.bacterium.D_5__uncultured.bacterium                                                                            NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__unidentified.rumen.bacterium.RF39.D_5__unidentified.rumen.bacterium.RF39                                                  NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.__.__                                                                                                                          NA
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Opitutales.D_4__Puniceicoccaceae.D_5__uncultured                                                                                     NA
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Verrucomicrobiales.D_4__Akkermansiaceae.D_5__Akkermansia                                                                             NA
##                                                                                                                                                                                            Std. Error
## (Intercept)                                                                                                                                                                                 2.036e+07
## AGE_CONSENT                                                                                                                                                                                 3.898e+04
## ANT_BMI                                                                                                                                                                                     5.309e+04
## PMRC_LAB_TRIG                                                                                                                                                                               8.788e+03
## PMRC_LAB_HDLCHOL                                                                                                                                                                            1.813e+05
## BP_SYSTOLIC_23                                                                                                                                                                              9.462e+04
## BP_DIASTOLIC_23                                                                                                                                                                             1.638e+05
## PMRC_LAB_GLU                                                                                                                                                                                1.616e+04
## PMRC_LAB_GH                                                                                                                                                                                 1.016e+06
## ANT_MEAS_WAIST_CM                                                                                                                                                                           8.796e+04
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria.D_3__Methanobacteriales.D_4__Methanobacteriaceae.D_5__Methanobrevibacter                                                               1.018e+09
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria.D_3__Methanobacteriales.D_4__Methanobacteriaceae.D_5__Methanosphaera                                                                   2.032e+10
## D_0__Archaea.D_1__Euryarchaeota.D_2__Thermoplasmata.D_3__Methanomassiliicoccales.D_4__Methanomassiliicoccaceae.D_5__Methanomassiliicoccus                                                   6.721e+10
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales.D_4__Actinomycetaceae.D_5__Actinomyces                                                                           3.530e+10
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales.D_4__Actinomycetaceae.D_5__Mobiluncus                                                                            1.659e+13
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales.D_4__Actinomycetaceae.D_5__Varibaculum                                                                           1.514e+11
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Bifidobacteriales.D_4__Bifidobacteriaceae.D_5__Bifidobacterium                                                                   5.128e+07
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Corynebacteriales.D_4__Corynebacteriaceae.D_5__Lawsonella                                                                        1.641e+13
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Micrococcales.D_4__Micrococcaceae.D_5__Rothia                                                                                    4.878e+10
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Atopobiaceae.D_5__Libanicoccus                                                                             7.526e+09
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Atopobiaceae.D_5__Olsenella                                                                                1.948e+11
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Coriobacteriaceae.D_5__Collinsella                                                                         4.363e+08
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Coriobacteriales.Incertae.Sedis.D_5__uncultured                                                            2.203e+09
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Adlercreutzia                                                                         1.504e+10
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__CHKCI002                                                                              3.877e+11
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Eggerthella                                                                           7.163e+08
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Enterorhabdus                                                                         1.665e+10
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Gordonibacter                                                                         5.048e+09
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Parvibacter                                                                           1.585e+09
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Senegalimassilia                                                                      8.408e+09
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Slackia                                                                               7.371e+09
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__uncultured                                                                            6.202e+09
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__uncultured.D_5__uncultured.bacterium                                                                       7.440e+09
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Bacteroidaceae.D_5__Bacteroides                                                                                   1.047e+07
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Barnesiellaceae.D_5__Barnesiella                                                                                  1.739e+08
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Barnesiellaceae.D_5__Coprobacter                                                                                  1.195e+09
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Barnesiellaceae.D_5__uncultured                                                                                   3.623e+10
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Dysgonomonadaceae.D_5__Dysgonomonas                                                                               1.065e+10
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Marinifilaceae.D_5__Butyricimonas                                                                                 8.951e+09
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Marinifilaceae.D_5__Odoribacter                                                                                   4.852e+08
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Marinifilaceae.D_5__Sanguibacteroides                                                                             2.477e+12
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__Muribaculum                                                                                          NA
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__metagenome                                                                                    1.250e+09
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__uncultured.Porphyromonadaceae.bacterium                                                       1.196e+10
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__uncultured.bacterium                                                                          4.234e+08
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__uncultured.organism                                                                           2.205e+09
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.__                                                                                                 4.860e+08
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Porphyromonadaceae.D_5__Porphyromonas                                                                             1.899e+10
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Alloprevotella                                                                                1.743e+08
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Paraprevotella                                                                                6.825e+07
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella                                                                                    8.421e+10
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella.2                                                                                  1.727e+08
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella.6                                                                                  4.238e+10
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella.7                                                                                  7.072e+07
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella.9                                                                                  6.615e+06
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotellaceae.NK3B31.group                                                                   1.493e+11
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotellaceae.UCG.001                                                                        2.396e+11
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__uncultured                                                                                    1.071e+09
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.__                                                                                                 1.141e+13
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae.D_5__Alistipes                                                                                      3.199e+07
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae.D_5__Millionella                                                                                    1.555e+13
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae.D_5__Rikenella                                                                                      2.387e+10
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae.D_5__Rikenellaceae.RC9.gut.group                                                                    1.301e+09
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Tannerellaceae.D_5__Parabacteroides                                                                               7.521e+07
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__uncultured.D_5__gut.metagenome                                                                                    2.538e+11
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__uncultured.D_5__uncultured.bacterium                                                                              2.680e+10
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.__.__                                                                                                                  1.166e+09
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Flavobacteriales.D_4__Flavobacteriaceae.D_5__uncultured                                                                              4.277e+09
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Sphingobacteriales.D_4__Sphingobacteriaceae.D_5__Sphingobacterium                                                                           NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__Candidatus.Gastranaerophilales.bacterium.Zag_111.D_5__Candidatus.Gastranaerophilales.bacterium.Zag_111         NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__Clostridium.sp..CAG.306.D_5__Clostridium.sp..CAG.306                                                           NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__uncultured.bacterium.D_5__uncultured.bacterium                                                          8.151e+08
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.__.__                                                                                                        8.274e+09
## D_0__Bacteria.D_1__Epsilonbacteraeota.D_2__Campylobacteria.D_3__Campylobacterales.D_4__Campylobacteraceae.D_5__Campylobacter                                                                6.243e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales.D_4__Family.XI.D_5__Gemella                                                                                                      7.803e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales.D_4__Staphylococcaceae.D_5__Staphylococcus                                                                                       9.659e+10
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Carnobacteriaceae.D_5__Carnobacterium                                                                                  9.070e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Carnobacteriaceae.D_5__Granulicatella                                                                                  1.755e+10
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Enterococcaceae.D_5__Enterococcus                                                                                      9.782e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Lactobacillaceae.D_5__Lactobacillus                                                                                    1.676e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Lactobacillaceae.D_5__Pediococcus                                                                                      6.810e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Leuconostocaceae.D_5__Leuconostoc                                                                                      1.031e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Leuconostocaceae.D_5__Weissella                                                                                        4.328e+10
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Streptococcaceae.D_5__Lactococcus                                                                                      5.860e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Streptococcaceae.D_5__Streptococcus                                                                                    7.601e+07
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae.D_5__Catabacter                                                                                   7.519e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae.D_5__Christensenellaceae.R.7.group                                                                1.514e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae.D_5__uncultured                                                                                   8.261e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae.__                                                                                                1.194e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiaceae.1.D_5__Clostridium.sensu.stricto.1                                                                     3.159e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiaceae.1.D_5__Clostridium.sensu.stricto.13                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__Clostridiales.bacterium.enrichment.culture.clone.06.1235251.67                     4.686e+12
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__gut.metagenome                                                                     5.920e+11
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__metagenome                                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__uncultured.Thermoanaerobacterales.bacterium                                        9.596e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__uncultured.bacterium                                                               2.057e+10
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__uncultured.organism                                                                1.693e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Defluviitaleaceae.D_5__Defluviitaleaceae.UCG.011                                                                      1.442e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Eubacteriaceae.D_5__Anaerofustis                                                                                      8.806e+10
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Eubacteriaceae.D_5__Eubacterium                                                                                       1.265e+10
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Anaerococcus                                                                                           1.424e+12
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Ezakiella                                                                                              3.487e+10
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Finegoldia                                                                                             1.400e+11
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Parvimonas                                                                                             3.976e+10
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Peptoniphilus                                                                                          7.399e+10
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__W5053                                                                                                  2.399e+13
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__Family.XIII.AD3011.group                                                                             4.319e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__Family.XIII.UCG.001                                                                                  8.592e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__Mogibacterium                                                                                        9.722e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__.Eubacterium..brachy.group                                                                           7.943e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__.Eubacterium..nodatum.group                                                                          6.538e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__uncultured                                                                                           3.410e+10
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.__                                                                                                        4.087e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Acetitomaculum                                                                                   9.592e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Agathobacter                                                                                     3.162e+07
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Anaerosporobacter                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Anaerostipes                                                                                     4.043e+07
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Blautia                                                                                          5.086e+06
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Butyrivibrio                                                                                     1.423e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__CAG.56                                                                                           3.459e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__CHKCI001                                                                                         2.070e+10
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Cellulosilyticum                                                                                 9.462e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Coprococcus.1                                                                                    2.976e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Coprococcus.2                                                                                    3.698e+07
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Coprococcus.3                                                                                    1.244e+08
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Cuneatibacter                                                                                    4.267e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Dorea                                                                                            7.308e+07
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Eisenbergiella                                                                                   2.931e+09
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Epulopiscium                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Fusicatenibacter                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__GCA.900066575                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__GCA.900066755                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Howardella                                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Hungatella                                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnoclostridium                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospira                                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.FCS020.group                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.ND3007.group                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.NK3A20.group                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.NK4A136.group                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.NK4B4.group                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.001                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.003                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.004                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.008                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.010                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lactonifactor                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Marvinbryantia                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Moryella                                                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Murimonas                                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Oribacterium                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Roseburia                                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Sellimonas                                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Shuttleworthia                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Tyzzerella                                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Tyzzerella.3                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Tyzzerella.4                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__UC5.1.2E3                                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..eligens.group                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..fissicatena.group                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..hallii.group                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..ruminantium.group                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..ventriosum.group                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..xylanophilum.group                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Ruminococcus..gauvreauii.group                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Ruminococcus..gnavus.group                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Ruminococcus..torques.group                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__uncultured                                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.__                                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptococcaceae.D_5__Peptococcus                                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptococcaceae.D_5__uncultured                                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Clostridioides                                                                                    NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Intestinibacter                                                                                   NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Paeniclostridium                                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Peptoclostridium                                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Peptostreptococcus                                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Romboutsia                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Terrisporobacter                                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Acetanaerobacterium                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Anaerofilum                                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Anaerotruncus                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Angelakisella                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Butyricicoccus                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__CAG.352                                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Candidatus.Soleaferrea                                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Caproiciproducens                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__DTU089                                                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Faecalibacterium                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Flavonifractor                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Fournierella                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__GCA.900066225                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Harryflintia                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Hydrogenoanaerobacterium                                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Intestinimonas                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Negativibacillus                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Oscillibacter                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Oscillospira                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Phocea                                                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Pseudoflavonifractor                                                                                    NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium.1                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium.5                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium.6                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium.9                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.NK4A214.group                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.002                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.003                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.004                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.005                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.007                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.008                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.009                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.010                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.013                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.014                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcus.1                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcus.2                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Subdoligranulum                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__UBA1819                                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__.Eubacterium..coprostanoligenes.group                                                                   NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__uncultured                                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.__                                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.__.__                                                                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.__.__.__                                                                                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Candidatus.Stoquefichus                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Catenibacterium                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Coprobacillus                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Dielma                                                                                   NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Erysipelatoclostridium                                                                   NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Erysipelotrichaceae.UCG.003                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Erysipelotrichaceae.UCG.004                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Faecalibaculum                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Faecalicoccus                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Faecalitalea                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Holdemanella                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Holdemania                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Merdibacter                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Solobacterium                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Turicibacter                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__.Clostridium..innocuum.group                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__uncultured                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.__                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Acidaminococcaceae.D_5__Acidaminococcus                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Acidaminococcaceae.D_5__Phascolarctobacterium                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Acidaminococcaceae.D_5__Succiniclasticum                                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Allisonella                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Anaeroglobus                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Anaerovibrio                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Dialister                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Megamonas                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Megasphaera                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Mitsuokella                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Veillonella                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__uncultured                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.__                                                                                                      NA
## D_0__Bacteria.D_1__Firmicutes.__.__.__.__                                                                                                                                                          NA
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia.D_3__Fusobacteriales.D_4__Fusobacteriaceae.D_5__Cetobacterium                                                                                   NA
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia.D_3__Fusobacteriales.D_4__Fusobacteriaceae.D_5__Fusobacterium                                                                                   NA
## D_0__Bacteria.D_1__Lentisphaerae.D_2__Lentisphaeria.D_3__Victivallales.D_4__Victivallaceae.D_5__Victivallis                                                                                        NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured.D_5__Azospirillum.sp..47_25                                                                       NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured.D_5__gut.metagenome                                                                               NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured.D_5__uncultured.bacterium                                                                         NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured.__                                                                                                NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.__.__.__                                                                                                                                NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae.D_5__Bilophila                                                                         NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae.D_5__Desulfovibrio                                                                     NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae.D_5__Mailhella                                                                         NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae.D_5__uncultured                                                                        NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Aeromonadales.D_4__Succinivibrionaceae.D_5__Succinivibrio                                                                          NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae.D_5__Comamonas                                                                         NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae.D_5__Parasutterella                                                                    NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae.D_5__Sutterella                                                                        NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae.__                                                                                     NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae.D_5__Escherichia.Shigella                                                                NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae.D_5__Klebsiella                                                                          NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae.D_5__Proteus                                                                             NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae.__                                                                                       NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pasteurellales.D_4__Pasteurellaceae.D_5__Haemophilus                                                                               NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pseudomonadales.D_4__Pseudomonadaceae.D_5__Pseudomonas                                                                             NA
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales.D_4__Synergistaceae.D_5__Cloacibacillus                                                                                       NA
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales.D_4__Synergistaceae.D_5__Fretibacterium                                                                                       NA
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales.D_4__Synergistaceae.D_5__Pyramidobacter                                                                                       NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales.D_4__gut.metagenome.D_5__gut.metagenome                                                                                       NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales.D_4__uncultured.organism.D_5__uncultured.organism                                                                             NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__Firmicutes.bacterium.CAG.822.D_5__Firmicutes.bacterium.CAG.822                                                            NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__gut.metagenome.D_5__gut.metagenome                                                                                        NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__uncultured.bacterium.adhufec202.D_5__uncultured.bacterium.adhufec202                                                      NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__uncultured.bacterium.D_5__uncultured.bacterium                                                                            NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__unidentified.rumen.bacterium.RF39.D_5__unidentified.rumen.bacterium.RF39                                                  NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.__.__                                                                                                                          NA
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Opitutales.D_4__Puniceicoccaceae.D_5__uncultured                                                                                     NA
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Verrucomicrobiales.D_4__Akkermansiaceae.D_5__Akkermansia                                                                             NA
##                                                                                                                                                                                            z value
## (Intercept)                                                                                                                                                                                      0
## AGE_CONSENT                                                                                                                                                                                      0
## ANT_BMI                                                                                                                                                                                          0
## PMRC_LAB_TRIG                                                                                                                                                                                    0
## PMRC_LAB_HDLCHOL                                                                                                                                                                                 0
## BP_SYSTOLIC_23                                                                                                                                                                                   0
## BP_DIASTOLIC_23                                                                                                                                                                                  0
## PMRC_LAB_GLU                                                                                                                                                                                     0
## PMRC_LAB_GH                                                                                                                                                                                      0
## ANT_MEAS_WAIST_CM                                                                                                                                                                                0
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria.D_3__Methanobacteriales.D_4__Methanobacteriaceae.D_5__Methanobrevibacter                                                                    0
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria.D_3__Methanobacteriales.D_4__Methanobacteriaceae.D_5__Methanosphaera                                                                        0
## D_0__Archaea.D_1__Euryarchaeota.D_2__Thermoplasmata.D_3__Methanomassiliicoccales.D_4__Methanomassiliicoccaceae.D_5__Methanomassiliicoccus                                                        0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales.D_4__Actinomycetaceae.D_5__Actinomyces                                                                                0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales.D_4__Actinomycetaceae.D_5__Mobiluncus                                                                                 0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales.D_4__Actinomycetaceae.D_5__Varibaculum                                                                                0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Bifidobacteriales.D_4__Bifidobacteriaceae.D_5__Bifidobacterium                                                                        0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Corynebacteriales.D_4__Corynebacteriaceae.D_5__Lawsonella                                                                             0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Micrococcales.D_4__Micrococcaceae.D_5__Rothia                                                                                         0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Atopobiaceae.D_5__Libanicoccus                                                                                  0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Atopobiaceae.D_5__Olsenella                                                                                     0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Coriobacteriaceae.D_5__Collinsella                                                                              0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Coriobacteriales.Incertae.Sedis.D_5__uncultured                                                                 0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Adlercreutzia                                                                              0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__CHKCI002                                                                                   0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Eggerthella                                                                                0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Enterorhabdus                                                                              0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Gordonibacter                                                                              0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Parvibacter                                                                                0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Senegalimassilia                                                                           0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Slackia                                                                                    0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__uncultured                                                                                 0
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__uncultured.D_5__uncultured.bacterium                                                                            0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Bacteroidaceae.D_5__Bacteroides                                                                                        0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Barnesiellaceae.D_5__Barnesiella                                                                                       0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Barnesiellaceae.D_5__Coprobacter                                                                                       0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Barnesiellaceae.D_5__uncultured                                                                                        0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Dysgonomonadaceae.D_5__Dysgonomonas                                                                                    0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Marinifilaceae.D_5__Butyricimonas                                                                                      0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Marinifilaceae.D_5__Odoribacter                                                                                        0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Marinifilaceae.D_5__Sanguibacteroides                                                                                  0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__Muribaculum                                                                                       NA
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__metagenome                                                                                         0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__uncultured.Porphyromonadaceae.bacterium                                                            0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__uncultured.bacterium                                                                               0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__uncultured.organism                                                                                0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.__                                                                                                      0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Porphyromonadaceae.D_5__Porphyromonas                                                                                  0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Alloprevotella                                                                                     0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Paraprevotella                                                                                     0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella                                                                                         0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella.2                                                                                       0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella.6                                                                                       0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella.7                                                                                       0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella.9                                                                                       0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotellaceae.NK3B31.group                                                                        0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotellaceae.UCG.001                                                                             0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__uncultured                                                                                         0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.__                                                                                                      0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae.D_5__Alistipes                                                                                           0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae.D_5__Millionella                                                                                         0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae.D_5__Rikenella                                                                                           0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae.D_5__Rikenellaceae.RC9.gut.group                                                                         0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Tannerellaceae.D_5__Parabacteroides                                                                                    0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__uncultured.D_5__gut.metagenome                                                                                         0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__uncultured.D_5__uncultured.bacterium                                                                                   0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.__.__                                                                                                                       0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Flavobacteriales.D_4__Flavobacteriaceae.D_5__uncultured                                                                                   0
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Sphingobacteriales.D_4__Sphingobacteriaceae.D_5__Sphingobacterium                                                                        NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__Candidatus.Gastranaerophilales.bacterium.Zag_111.D_5__Candidatus.Gastranaerophilales.bacterium.Zag_111      NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__Clostridium.sp..CAG.306.D_5__Clostridium.sp..CAG.306                                                        NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__uncultured.bacterium.D_5__uncultured.bacterium                                                               0
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.__.__                                                                                                             0
## D_0__Bacteria.D_1__Epsilonbacteraeota.D_2__Campylobacteria.D_3__Campylobacterales.D_4__Campylobacteraceae.D_5__Campylobacter                                                                     0
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales.D_4__Family.XI.D_5__Gemella                                                                                                           0
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales.D_4__Staphylococcaceae.D_5__Staphylococcus                                                                                            0
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Carnobacteriaceae.D_5__Carnobacterium                                                                                       0
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Carnobacteriaceae.D_5__Granulicatella                                                                                       0
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Enterococcaceae.D_5__Enterococcus                                                                                           0
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Lactobacillaceae.D_5__Lactobacillus                                                                                         0
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Lactobacillaceae.D_5__Pediococcus                                                                                           0
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Leuconostocaceae.D_5__Leuconostoc                                                                                           0
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Leuconostocaceae.D_5__Weissella                                                                                             0
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Streptococcaceae.D_5__Lactococcus                                                                                           0
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Streptococcaceae.D_5__Streptococcus                                                                                         0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae.D_5__Catabacter                                                                                        0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae.D_5__Christensenellaceae.R.7.group                                                                     0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae.D_5__uncultured                                                                                        0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae.__                                                                                                     0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiaceae.1.D_5__Clostridium.sensu.stricto.1                                                                          0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiaceae.1.D_5__Clostridium.sensu.stricto.13                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__Clostridiales.bacterium.enrichment.culture.clone.06.1235251.67                          0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__gut.metagenome                                                                          0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__metagenome                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__uncultured.Thermoanaerobacterales.bacterium                                             0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__uncultured.bacterium                                                                    0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__uncultured.organism                                                                     0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Defluviitaleaceae.D_5__Defluviitaleaceae.UCG.011                                                                           0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Eubacteriaceae.D_5__Anaerofustis                                                                                           0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Eubacteriaceae.D_5__Eubacterium                                                                                            0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Anaerococcus                                                                                                0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Ezakiella                                                                                                   0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Finegoldia                                                                                                  0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Parvimonas                                                                                                  0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Peptoniphilus                                                                                               0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__W5053                                                                                                       0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__Family.XIII.AD3011.group                                                                                  0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__Family.XIII.UCG.001                                                                                       0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__Mogibacterium                                                                                             0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__.Eubacterium..brachy.group                                                                                0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__.Eubacterium..nodatum.group                                                                               0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__uncultured                                                                                                0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.__                                                                                                             0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Acetitomaculum                                                                                        0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Agathobacter                                                                                          0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Anaerosporobacter                                                                                    NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Anaerostipes                                                                                          0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Blautia                                                                                               0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Butyrivibrio                                                                                          0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__CAG.56                                                                                                0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__CHKCI001                                                                                              0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Cellulosilyticum                                                                                      0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Coprococcus.1                                                                                         0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Coprococcus.2                                                                                         0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Coprococcus.3                                                                                         0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Cuneatibacter                                                                                         0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Dorea                                                                                                 0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Eisenbergiella                                                                                        0
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Epulopiscium                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Fusicatenibacter                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__GCA.900066575                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__GCA.900066755                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Howardella                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Hungatella                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnoclostridium                                                                                    NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospira                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.FCS020.group                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.ND3007.group                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.NK3A20.group                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.NK4A136.group                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.NK4B4.group                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.001                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.003                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.004                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.008                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.010                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lactonifactor                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Marvinbryantia                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Moryella                                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Murimonas                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Oribacterium                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Roseburia                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Sellimonas                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Shuttleworthia                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Tyzzerella                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Tyzzerella.3                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Tyzzerella.4                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__UC5.1.2E3                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..eligens.group                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..fissicatena.group                                                                      NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..hallii.group                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..ruminantium.group                                                                      NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..ventriosum.group                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..xylanophilum.group                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Ruminococcus..gauvreauii.group                                                                      NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Ruminococcus..gnavus.group                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Ruminococcus..torques.group                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__uncultured                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.__                                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptococcaceae.D_5__Peptococcus                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptococcaceae.D_5__uncultured                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Clostridioides                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Intestinibacter                                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Paeniclostridium                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Peptoclostridium                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Peptostreptococcus                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Romboutsia                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Terrisporobacter                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Acetanaerobacterium                                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Anaerofilum                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Anaerotruncus                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Angelakisella                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Butyricicoccus                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__CAG.352                                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Candidatus.Soleaferrea                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Caproiciproducens                                                                                    NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__DTU089                                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Faecalibacterium                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Flavonifractor                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Fournierella                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__GCA.900066225                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Harryflintia                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Hydrogenoanaerobacterium                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Intestinimonas                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Negativibacillus                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Oscillibacter                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Oscillospira                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Phocea                                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Pseudoflavonifractor                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium                                                                                    NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium.1                                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium.5                                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium.6                                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium.9                                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.NK4A214.group                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.002                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.003                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.004                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.005                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.007                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.008                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.009                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.010                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.013                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.014                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcus.1                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcus.2                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Subdoligranulum                                                                                      NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__UBA1819                                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__.Eubacterium..coprostanoligenes.group                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__uncultured                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.__                                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.__.__                                                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.__.__.__                                                                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Candidatus.Stoquefichus                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Catenibacterium                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Coprobacillus                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Dielma                                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Erysipelatoclostridium                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Erysipelotrichaceae.UCG.003                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Erysipelotrichaceae.UCG.004                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Faecalibaculum                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Faecalicoccus                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Faecalitalea                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Holdemanella                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Holdemania                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Merdibacter                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Solobacterium                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Turicibacter                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__.Clostridium..innocuum.group                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__uncultured                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.__                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Acidaminococcaceae.D_5__Acidaminococcus                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Acidaminococcaceae.D_5__Phascolarctobacterium                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Acidaminococcaceae.D_5__Succiniclasticum                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Allisonella                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Anaeroglobus                                                                                    NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Anaerovibrio                                                                                    NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Dialister                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Megamonas                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Megasphaera                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Mitsuokella                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Veillonella                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__uncultured                                                                                      NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.__                                                                                                   NA
## D_0__Bacteria.D_1__Firmicutes.__.__.__.__                                                                                                                                                       NA
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia.D_3__Fusobacteriales.D_4__Fusobacteriaceae.D_5__Cetobacterium                                                                                NA
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia.D_3__Fusobacteriales.D_4__Fusobacteriaceae.D_5__Fusobacterium                                                                                NA
## D_0__Bacteria.D_1__Lentisphaerae.D_2__Lentisphaeria.D_3__Victivallales.D_4__Victivallaceae.D_5__Victivallis                                                                                     NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured.D_5__Azospirillum.sp..47_25                                                                    NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured.D_5__gut.metagenome                                                                            NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured.D_5__uncultured.bacterium                                                                      NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured.__                                                                                             NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.__.__.__                                                                                                                             NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae.D_5__Bilophila                                                                      NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae.D_5__Desulfovibrio                                                                  NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae.D_5__Mailhella                                                                      NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae.D_5__uncultured                                                                     NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Aeromonadales.D_4__Succinivibrionaceae.D_5__Succinivibrio                                                                       NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae.D_5__Comamonas                                                                      NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae.D_5__Parasutterella                                                                 NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae.D_5__Sutterella                                                                     NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae.__                                                                                  NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae.D_5__Escherichia.Shigella                                                             NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae.D_5__Klebsiella                                                                       NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae.D_5__Proteus                                                                          NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae.__                                                                                    NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pasteurellales.D_4__Pasteurellaceae.D_5__Haemophilus                                                                            NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pseudomonadales.D_4__Pseudomonadaceae.D_5__Pseudomonas                                                                          NA
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales.D_4__Synergistaceae.D_5__Cloacibacillus                                                                                    NA
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales.D_4__Synergistaceae.D_5__Fretibacterium                                                                                    NA
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales.D_4__Synergistaceae.D_5__Pyramidobacter                                                                                    NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales.D_4__gut.metagenome.D_5__gut.metagenome                                                                                    NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales.D_4__uncultured.organism.D_5__uncultured.organism                                                                          NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__Firmicutes.bacterium.CAG.822.D_5__Firmicutes.bacterium.CAG.822                                                         NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__gut.metagenome.D_5__gut.metagenome                                                                                     NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__uncultured.bacterium.adhufec202.D_5__uncultured.bacterium.adhufec202                                                   NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__uncultured.bacterium.D_5__uncultured.bacterium                                                                         NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__unidentified.rumen.bacterium.RF39.D_5__unidentified.rumen.bacterium.RF39                                               NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.__.__                                                                                                                       NA
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Opitutales.D_4__Puniceicoccaceae.D_5__uncultured                                                                                  NA
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Verrucomicrobiales.D_4__Akkermansiaceae.D_5__Akkermansia                                                                          NA
##                                                                                                                                                                                            Pr(>|z|)
## (Intercept)                                                                                                                                                                                       1
## AGE_CONSENT                                                                                                                                                                                       1
## ANT_BMI                                                                                                                                                                                           1
## PMRC_LAB_TRIG                                                                                                                                                                                     1
## PMRC_LAB_HDLCHOL                                                                                                                                                                                  1
## BP_SYSTOLIC_23                                                                                                                                                                                    1
## BP_DIASTOLIC_23                                                                                                                                                                                   1
## PMRC_LAB_GLU                                                                                                                                                                                      1
## PMRC_LAB_GH                                                                                                                                                                                       1
## ANT_MEAS_WAIST_CM                                                                                                                                                                                 1
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria.D_3__Methanobacteriales.D_4__Methanobacteriaceae.D_5__Methanobrevibacter                                                                     1
## D_0__Archaea.D_1__Euryarchaeota.D_2__Methanobacteria.D_3__Methanobacteriales.D_4__Methanobacteriaceae.D_5__Methanosphaera                                                                         1
## D_0__Archaea.D_1__Euryarchaeota.D_2__Thermoplasmata.D_3__Methanomassiliicoccales.D_4__Methanomassiliicoccaceae.D_5__Methanomassiliicoccus                                                         1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales.D_4__Actinomycetaceae.D_5__Actinomyces                                                                                 1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales.D_4__Actinomycetaceae.D_5__Mobiluncus                                                                                  1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Actinomycetales.D_4__Actinomycetaceae.D_5__Varibaculum                                                                                 1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Bifidobacteriales.D_4__Bifidobacteriaceae.D_5__Bifidobacterium                                                                         1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Corynebacteriales.D_4__Corynebacteriaceae.D_5__Lawsonella                                                                              1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Actinobacteria.D_3__Micrococcales.D_4__Micrococcaceae.D_5__Rothia                                                                                          1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Atopobiaceae.D_5__Libanicoccus                                                                                   1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Atopobiaceae.D_5__Olsenella                                                                                      1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Coriobacteriaceae.D_5__Collinsella                                                                               1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Coriobacteriales.Incertae.Sedis.D_5__uncultured                                                                  1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Adlercreutzia                                                                               1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__CHKCI002                                                                                    1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Eggerthella                                                                                 1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Enterorhabdus                                                                               1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Gordonibacter                                                                               1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Parvibacter                                                                                 1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Senegalimassilia                                                                            1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__Slackia                                                                                     1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__Eggerthellaceae.D_5__uncultured                                                                                  1
## D_0__Bacteria.D_1__Actinobacteria.D_2__Coriobacteriia.D_3__Coriobacteriales.D_4__uncultured.D_5__uncultured.bacterium                                                                             1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Bacteroidaceae.D_5__Bacteroides                                                                                         1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Barnesiellaceae.D_5__Barnesiella                                                                                        1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Barnesiellaceae.D_5__Coprobacter                                                                                        1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Barnesiellaceae.D_5__uncultured                                                                                         1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Dysgonomonadaceae.D_5__Dysgonomonas                                                                                     1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Marinifilaceae.D_5__Butyricimonas                                                                                       1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Marinifilaceae.D_5__Odoribacter                                                                                         1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Marinifilaceae.D_5__Sanguibacteroides                                                                                   1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__Muribaculum                                                                                        NA
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__metagenome                                                                                          1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__uncultured.Porphyromonadaceae.bacterium                                                             1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__uncultured.bacterium                                                                                1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.D_5__uncultured.organism                                                                                 1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Muribaculaceae.__                                                                                                       1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Porphyromonadaceae.D_5__Porphyromonas                                                                                   1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Alloprevotella                                                                                      1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Paraprevotella                                                                                      1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella                                                                                          1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella.2                                                                                        1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella.6                                                                                        1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella.7                                                                                        1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotella.9                                                                                        1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotellaceae.NK3B31.group                                                                         1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__Prevotellaceae.UCG.001                                                                              1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.D_5__uncultured                                                                                          1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Prevotellaceae.__                                                                                                       1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae.D_5__Alistipes                                                                                            1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae.D_5__Millionella                                                                                          1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae.D_5__Rikenella                                                                                            1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Rikenellaceae.D_5__Rikenellaceae.RC9.gut.group                                                                          1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__Tannerellaceae.D_5__Parabacteroides                                                                                     1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__uncultured.D_5__gut.metagenome                                                                                          1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.D_4__uncultured.D_5__uncultured.bacterium                                                                                    1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Bacteroidales.__.__                                                                                                                        1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Flavobacteriales.D_4__Flavobacteriaceae.D_5__uncultured                                                                                    1
## D_0__Bacteria.D_1__Bacteroidetes.D_2__Bacteroidia.D_3__Sphingobacteriales.D_4__Sphingobacteriaceae.D_5__Sphingobacterium                                                                         NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__Candidatus.Gastranaerophilales.bacterium.Zag_111.D_5__Candidatus.Gastranaerophilales.bacterium.Zag_111       NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__Clostridium.sp..CAG.306.D_5__Clostridium.sp..CAG.306                                                         NA
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.D_4__uncultured.bacterium.D_5__uncultured.bacterium                                                                1
## D_0__Bacteria.D_1__Cyanobacteria.D_2__Melainabacteria.D_3__Gastranaerophilales.__.__                                                                                                              1
## D_0__Bacteria.D_1__Epsilonbacteraeota.D_2__Campylobacteria.D_3__Campylobacterales.D_4__Campylobacteraceae.D_5__Campylobacter                                                                      1
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales.D_4__Family.XI.D_5__Gemella                                                                                                            1
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Bacillales.D_4__Staphylococcaceae.D_5__Staphylococcus                                                                                             1
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Carnobacteriaceae.D_5__Carnobacterium                                                                                        1
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Carnobacteriaceae.D_5__Granulicatella                                                                                        1
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Enterococcaceae.D_5__Enterococcus                                                                                            1
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Lactobacillaceae.D_5__Lactobacillus                                                                                          1
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Lactobacillaceae.D_5__Pediococcus                                                                                            1
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Leuconostocaceae.D_5__Leuconostoc                                                                                            1
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Leuconostocaceae.D_5__Weissella                                                                                              1
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Streptococcaceae.D_5__Lactococcus                                                                                            1
## D_0__Bacteria.D_1__Firmicutes.D_2__Bacilli.D_3__Lactobacillales.D_4__Streptococcaceae.D_5__Streptococcus                                                                                          1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae.D_5__Catabacter                                                                                         1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae.D_5__Christensenellaceae.R.7.group                                                                      1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae.D_5__uncultured                                                                                         1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Christensenellaceae.__                                                                                                      1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiaceae.1.D_5__Clostridium.sensu.stricto.1                                                                           1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiaceae.1.D_5__Clostridium.sensu.stricto.13                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__Clostridiales.bacterium.enrichment.culture.clone.06.1235251.67                           1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__gut.metagenome                                                                           1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__metagenome                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__uncultured.Thermoanaerobacterales.bacterium                                              1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__uncultured.bacterium                                                                     1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Clostridiales.vadinBB60.group.D_5__uncultured.organism                                                                      1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Defluviitaleaceae.D_5__Defluviitaleaceae.UCG.011                                                                            1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Eubacteriaceae.D_5__Anaerofustis                                                                                            1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Eubacteriaceae.D_5__Eubacterium                                                                                             1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Anaerococcus                                                                                                 1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Ezakiella                                                                                                    1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Finegoldia                                                                                                   1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Parvimonas                                                                                                   1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__Peptoniphilus                                                                                                1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XI.D_5__W5053                                                                                                        1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__Family.XIII.AD3011.group                                                                                   1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__Family.XIII.UCG.001                                                                                        1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__Mogibacterium                                                                                              1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__.Eubacterium..brachy.group                                                                                 1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__.Eubacterium..nodatum.group                                                                                1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.D_5__uncultured                                                                                                 1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Family.XIII.__                                                                                                              1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Acetitomaculum                                                                                         1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Agathobacter                                                                                           1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Anaerosporobacter                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Anaerostipes                                                                                           1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Blautia                                                                                                1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Butyrivibrio                                                                                           1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__CAG.56                                                                                                 1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__CHKCI001                                                                                               1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Cellulosilyticum                                                                                       1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Coprococcus.1                                                                                          1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Coprococcus.2                                                                                          1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Coprococcus.3                                                                                          1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Cuneatibacter                                                                                          1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Dorea                                                                                                  1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Eisenbergiella                                                                                         1
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Epulopiscium                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Fusicatenibacter                                                                                      NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__GCA.900066575                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__GCA.900066755                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Howardella                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Hungatella                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnoclostridium                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospira                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.FCS020.group                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.ND3007.group                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.NK3A20.group                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.NK4A136.group                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.NK4B4.group                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.001                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.003                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.004                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.008                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lachnospiraceae.UCG.010                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Lactonifactor                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Marvinbryantia                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Moryella                                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Murimonas                                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Oribacterium                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Roseburia                                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Sellimonas                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Shuttleworthia                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Tyzzerella                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Tyzzerella.3                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__Tyzzerella.4                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__UC5.1.2E3                                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..eligens.group                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..fissicatena.group                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..hallii.group                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..ruminantium.group                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..ventriosum.group                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Eubacterium..xylanophilum.group                                                                      NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Ruminococcus..gauvreauii.group                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Ruminococcus..gnavus.group                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__.Ruminococcus..torques.group                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.D_5__uncultured                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Lachnospiraceae.__                                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptococcaceae.D_5__Peptococcus                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptococcaceae.D_5__uncultured                                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Clostridioides                                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Intestinibacter                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Paeniclostridium                                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Peptoclostridium                                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Peptostreptococcus                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Romboutsia                                                                                      NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Peptostreptococcaceae.D_5__Terrisporobacter                                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Acetanaerobacterium                                                                                   NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Anaerofilum                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Anaerotruncus                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Angelakisella                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Butyricicoccus                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__CAG.352                                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Candidatus.Soleaferrea                                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Caproiciproducens                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__DTU089                                                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Faecalibacterium                                                                                      NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Flavonifractor                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Fournierella                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__GCA.900066225                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Harryflintia                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Hydrogenoanaerobacterium                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Intestinimonas                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Negativibacillus                                                                                      NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Oscillibacter                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Oscillospira                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Phocea                                                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Pseudoflavonifractor                                                                                  NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium.1                                                                                   NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium.5                                                                                   NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium.6                                                                                   NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminiclostridium.9                                                                                   NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.NK4A214.group                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.002                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.003                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.004                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.005                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.007                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.008                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.009                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.010                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.013                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcaceae.UCG.014                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcus.1                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Ruminococcus.2                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__Subdoligranulum                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__UBA1819                                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__.Eubacterium..coprostanoligenes.group                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.D_5__uncultured                                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.D_4__Ruminococcaceae.__                                                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.D_3__Clostridiales.__.__                                                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Clostridia.__.__.__                                                                                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Candidatus.Stoquefichus                                                                NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Catenibacterium                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Coprobacillus                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Dielma                                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Erysipelatoclostridium                                                                 NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Erysipelotrichaceae.UCG.003                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Erysipelotrichaceae.UCG.004                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Faecalibaculum                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Faecalicoccus                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Faecalitalea                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Holdemanella                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Holdemania                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Merdibacter                                                                            NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Solobacterium                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__Turicibacter                                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__.Clostridium..innocuum.group                                                           NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.D_5__uncultured                                                                             NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Erysipelotrichia.D_3__Erysipelotrichales.D_4__Erysipelotrichaceae.__                                                                                          NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Acidaminococcaceae.D_5__Acidaminococcus                                                                               NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Acidaminococcaceae.D_5__Phascolarctobacterium                                                                         NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Acidaminococcaceae.D_5__Succiniclasticum                                                                              NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Allisonella                                                                                      NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Anaeroglobus                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Anaerovibrio                                                                                     NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Dialister                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Megamonas                                                                                        NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Megasphaera                                                                                      NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Mitsuokella                                                                                      NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__Veillonella                                                                                      NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.D_5__uncultured                                                                                       NA
## D_0__Bacteria.D_1__Firmicutes.D_2__Negativicutes.D_3__Selenomonadales.D_4__Veillonellaceae.__                                                                                                    NA
## D_0__Bacteria.D_1__Firmicutes.__.__.__.__                                                                                                                                                        NA
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia.D_3__Fusobacteriales.D_4__Fusobacteriaceae.D_5__Cetobacterium                                                                                 NA
## D_0__Bacteria.D_1__Fusobacteria.D_2__Fusobacteriia.D_3__Fusobacteriales.D_4__Fusobacteriaceae.D_5__Fusobacterium                                                                                 NA
## D_0__Bacteria.D_1__Lentisphaerae.D_2__Lentisphaeria.D_3__Victivallales.D_4__Victivallaceae.D_5__Victivallis                                                                                      NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured.D_5__Azospirillum.sp..47_25                                                                     NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured.D_5__gut.metagenome                                                                             NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured.D_5__uncultured.bacterium                                                                       NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.D_3__Rhodospirillales.D_4__uncultured.__                                                                                              NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Alphaproteobacteria.__.__.__                                                                                                                              NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae.D_5__Bilophila                                                                       NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae.D_5__Desulfovibrio                                                                   NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae.D_5__Mailhella                                                                       NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Deltaproteobacteria.D_3__Desulfovibrionales.D_4__Desulfovibrionaceae.D_5__uncultured                                                                      NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Aeromonadales.D_4__Succinivibrionaceae.D_5__Succinivibrio                                                                        NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae.D_5__Comamonas                                                                       NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae.D_5__Parasutterella                                                                  NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae.D_5__Sutterella                                                                      NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Betaproteobacteriales.D_4__Burkholderiaceae.__                                                                                   NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae.D_5__Escherichia.Shigella                                                              NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae.D_5__Klebsiella                                                                        NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae.D_5__Proteus                                                                           NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Enterobacteriales.D_4__Enterobacteriaceae.__                                                                                     NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pasteurellales.D_4__Pasteurellaceae.D_5__Haemophilus                                                                             NA
## D_0__Bacteria.D_1__Proteobacteria.D_2__Gammaproteobacteria.D_3__Pseudomonadales.D_4__Pseudomonadaceae.D_5__Pseudomonas                                                                           NA
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales.D_4__Synergistaceae.D_5__Cloacibacillus                                                                                     NA
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales.D_4__Synergistaceae.D_5__Fretibacterium                                                                                     NA
## D_0__Bacteria.D_1__Synergistetes.D_2__Synergistia.D_3__Synergistales.D_4__Synergistaceae.D_5__Pyramidobacter                                                                                     NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales.D_4__gut.metagenome.D_5__gut.metagenome                                                                                     NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Izimaplasmatales.D_4__uncultured.organism.D_5__uncultured.organism                                                                           NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__Firmicutes.bacterium.CAG.822.D_5__Firmicutes.bacterium.CAG.822                                                          NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__gut.metagenome.D_5__gut.metagenome                                                                                      NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__uncultured.bacterium.adhufec202.D_5__uncultured.bacterium.adhufec202                                                    NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__uncultured.bacterium.D_5__uncultured.bacterium                                                                          NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.D_4__unidentified.rumen.bacterium.RF39.D_5__unidentified.rumen.bacterium.RF39                                                NA
## D_0__Bacteria.D_1__Tenericutes.D_2__Mollicutes.D_3__Mollicutes.RF39.__.__                                                                                                                        NA
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Opitutales.D_4__Puniceicoccaceae.D_5__uncultured                                                                                   NA
## D_0__Bacteria.D_1__Verrucomicrobia.D_2__Verrucomicrobiae.D_3__Verrucomicrobiales.D_4__Akkermansiaceae.D_5__Akkermansia                                                                           NA
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 1.6707e+02  on 120  degrees of freedom
## Residual deviance: 7.0199e-10  on   0  degrees of freedom
##   (167 observations deleted due to missingness)
## AIC: 242
## 
## Number of Fisher Scoring iterations: 25
#Male
# the code below checks the sum of all numeric cols and removes any cols that sum to zero
colsums_male <- colSums(Filter(is.numeric,merged.table_male))
zero_cols <- names(colsums_male[colsums_male==0 & !is.na(colsums_male)])
# re-define merged.tale without cols that sum to zero
merged.table_male <- merged.table_male %>% select(-one_of(zero_cols))

#Female
# the code below checks the sum of all numeric cols and removes any cols that sum to zero
colsums_female <- colSums(Filter(is.numeric,merged.table_female))
zero_cols <- names(colsums_female[colsums_female==0 & !is.na(colsums_female)])
# re-define merged.tale without cols that sum to zero
merged.table_female <- merged.table_female %>% select(-one_of(zero_cols))

#Correlation test

multi_assoc <- function(mdf,exp_vars, res_vars, p.zeros=.25,adj.zero=TRUE,method, inc.zeros=TRUE, run_ratio = TRUE){
  #Arguments:
  # mdf - dataframe where the explanitory and response variables are as columns and subjects are rows
  # exp_vars - a vector of numbers that indicate the explanitory variable cols in mdf 
  # res_vars - a vector of numbers that indicate the response variable cols in mdf
  # p.zeros - the max amount of zeros in a singe variable that will be tolerated (expressed as a percent)
  # this taxa has to be 25% present in all samples to run the analysis.
  # adj.zeros - add a small value to each datapoint (0.1% of the variable average) to allow for divide by zero
  # add small number, so it's close to 0 but has some values (if running correlation with 0, causes problems)
  # method - 'spearman', 'pearson'
  # spearman brings values high to low [ranking]; whereas pearson uses the actual values; spearman corrects/reduces variation but p value less significant.
  # inc.zeros - TRUE = include all zeros in exp_vars for analysis. FALSE = replace all zeros wtih NA
  # run_ration - TRUE = it will run correlations for every exp_var1:exp_var2 combination to the response variable. If not "TRUE", will only run correlations with exp_var1 vs res_var
  
  
  
  # modification of multi_assoc(method = 'spearman', ). Only divides and multiplys explanitory variables
  if (inc.zeros==FALSE){
    mdf[,exp_vars] <- apply(mdf[,exp_vars], 2, function(x) ifelse(x == 0, NA, x))
  }
  mdf$None <- c(rep(1,nrow(mdf)))
  exp_vars <- c(exp_vars,match('None', colnames(mdf)))
  d <- list()
  n <- 0
  t=1
  col_headers <- c("Explanitory_var1","Explanitory_var2","Response_var", "Estimate", "c.Pval", "Rsq", 'r.Pval')
  if(adj.zero == TRUE){ #check to see if adjustment was specified
    adj=1
  }else{
    adj=0
  }
  for (i in exp_vars[-length(exp_vars)]) { #for every exp variable. This excludes the "None" column added in line above
    if ((length(which(mdf[,i]==0|is.na(mdf[,i])==TRUE))<p.zeros*length(mdf[,i])) & (is.numeric(mdf[,i])==TRUE)){ # if the percent of zeros in exp var is less than the specified p.zero threshold, continue, else skip exp var
      if (run_ratio == TRUE){
        list2 <- exp_vars[-match(i, exp_vars)] #makes a list of all variables except for "i" variable to loop over (for divide only, see multiply below)
      } else {
        list2 <- 'None'
      }
      for (j in list2){
        if ((length(which(mdf[,j]==0|is.na(mdf[,j])==TRUE))<p.zeros*length(mdf[,j])) & (is.numeric(mdf[,j])==TRUE)){ #check to see if comparison exp var meets p.zero threshold
          for (x in res_vars){ #loops over every response variable
            #run tests
            z <- (mdf[,i]+adj*(0.001*mean(mdf[,i],na.rm = T)))/(mdf[,j]+adj*(0.001*mean(mdf[,j],na.rm = T)))
            z[is.infinite(z)] <- NA
            y <- mdf[,x]
            tmp <- cor.test(y, z, method = method)
            reg <- summary(lm(y~z))
            tmp_df <- data.frame(
              colnames(mdf[i]),
              colnames(mdf[j]),
              colnames(mdf[x]),
              as.numeric(tmp[4]), 
              as.numeric(tmp[3]),
              as.numeric(reg$r.squared),
              as.numeric(try(pf(reg$fstatistic[1],reg$fstatistic[2],reg$fstatistic[3], lower.tail = F),silent = T)),
              stringsAsFactors = FALSE)
            n <- n+1
            d[[n]] <- tmp_df
          }
        }
      }
    }
    if (t > (length(exp_vars)/100)){ # prints status as a percentage
      print(paste(match(i,exp_vars)/length(exp_vars)*100,"%"))
      t=1
    }else{
      t=t+1
    }
  }
  tmp_results <- do.call(rbind,d)
  colnames(tmp_results) <- col_headers
  tmp_results <- as_data_frame(tmp_results)
  tmp_results$c.fdr <- p.adjust(tmp_results$c.Pval)
  cp <- match("c.Pval", colnames(tmp_results))
  tmp_results <- tmp_results[,c(1:cp, ncol(tmp_results),(cp+1):(ncol(tmp_results)-1))]
  tmp_results$r.fdr <- p.adjust(tmp_results$r.Pval)
  multi_corr_tbl <- tmp_results[order(tmp_results$c.Pval, decreasing = F),]
  rownames(multi_corr_tbl) <- c(1:nrow(multi_corr_tbl))
  multi_corr_tbl$index <- c(1:nrow(multi_corr_tbl))
  if (run_ratio != TRUE){
    multi_corr_tbl <- multi_corr_tbl[,-2]
  }
  return(multi_corr_tbl)
}

#####################################
#####################################

plot_comprsn <- function (data_tbl,comp_tbl,row,color.by='All samples'){
  #Arguments:
  # data_tbl - dataframe where the explanitory and response variables are as columns and subjects are rows (same df used in multi_pred_cor())
  # comp_tbl - comparison table, this is the output of multi_pred_cor()
  # row - the row of the comp_tbl you want to plot (row 1 is the most significant correlation)
  # color.by - the col of data_table to use as input for aes(color =). Must specify the col with $.
  
  
  
  
  if (colnames(comp_tbl[2]) != "Explanitory_var2"){
    tops <- c(comp_tbl[[row,1]], "", comp_tbl[[row,2]])
    z=data_tbl[[tops[1]]]
    label <- tops[1]
  } else {
    tops <- c(comp_tbl[[row,1]], comp_tbl[[row,2]], comp_tbl[[row,3]])
    if (tops[2]=="None"){
      z=data_tbl[[tops[1]]]
      label <- tops[1]
    } else {
      z <- do.call('/',list(data_tbl[[tops[1]]],data_tbl[[tops[2]]]))
      z[is.infinite(z)] <- NA
      label <- paste(tops[1], tops[2], sep = paste("_##","/","##_"))
    }
  }
  y <- tops[3]
  data_tbl$zn <- z
  x <- 'zn'
  my.formula <- x~y
  
  if (color.by != "All samples"){
    color.by <- data_tbl[,color.by]
    colors <- scale_color_brewer(palette="Set1")
  } else {
    colors <- scale_color_manual(values = 'black')
  }
  
  plot <- data_tbl %>% ggplot(aes(x = data_tbl$zn, y = data_tbl[,y], color=color.by))+
    xlab(label)+
    ylab(tops[3])+
    geom_point()+
    colors+
    stat_cor(method = 'spearman', label.y.npc = .95)+
    geom_smooth(method=lm, se=F)
  
  return(plot)
}

#Scaterplot and heatmap ##BMI

#Try each phenotype of the disease: phe = c(6:12,14,15)
phe = c(5) #BMI
#phe = c(6) #TRIG
# phe = c(7) #HDL
# phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:285) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.12359550561798 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "2.24719101123596 %"
## [1] "3.37078651685393 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.49438202247191 %"
## [1] "5.61797752808989 %"
## [1] "6.74157303370786 %"
## [1] "7.86516853932584 %"
## [1] "8.98876404494382 %"
## [1] "10.1123595505618 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "11.2359550561798 %"
## [1] "12.3595505617978 %"
## [1] "13.4831460674157 %"
## [1] "14.6067415730337 %"
## [1] "15.7303370786517 %"
## [1] "16.8539325842697 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "17.9775280898876 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.1011235955056 %"
## [1] "20.2247191011236 %"
## [1] "21.3483146067416 %"
## [1] "22.4719101123595 %"
## [1] "23.5955056179775 %"
## [1] "24.7191011235955 %"
## [1] "25.8426966292135 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.9662921348315 %"
## [1] "28.0898876404494 %"
## [1] "29.2134831460674 %"
## [1] "30.3370786516854 %"
## [1] "31.4606741573034 %"
## [1] "32.5842696629214 %"
## [1] "33.7078651685393 %"
## [1] "34.8314606741573 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "35.9550561797753 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "37.0786516853933 %"
## [1] "38.2022471910112 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3258426966292 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "40.4494382022472 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "41.5730337078652 %"
## [1] "42.6966292134831 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "43.8202247191011 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "44.9438202247191 %"
## [1] "46.0674157303371 %"
## [1] "47.1910112359551 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.314606741573 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.438202247191 %"
## [1] "50.561797752809 %"
## [1] "51.685393258427 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "52.8089887640449 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.9325842696629 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "55.0561797752809 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "56.1797752808989 %"
## [1] "57.3033707865169 %"
## [1] "58.4269662921348 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "59.5505617977528 %"
## [1] "60.6741573033708 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.7977528089888 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.9213483146067 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "64.0449438202247 %"
## [1] "65.1685393258427 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "66.2921348314607 %"
## [1] "67.4157303370787 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.5393258426966 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.6629213483146 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "70.7865168539326 %"
## [1] "71.9101123595506 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "73.0337078651685 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "74.1573033707865 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.2808988764045 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.4044943820225 %"
## [1] "77.5280898876404 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "78.6516853932584 %"
## [1] "79.7752808988764 %"
## [1] "80.8988764044944 %"
## [1] "82.0224719101124 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "83.1460674157303 %"
## [1] "84.2696629213483 %"
## [1] "85.3932584269663 %"
## [1] "86.5168539325843 %"
## [1] "87.6404494382023 %"
## [1] "88.7640449438202 %"
## [1] "89.8876404494382 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "91.0112359550562 %"
## [1] "92.1348314606742 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "93.2584269662921 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "94.3820224719101 %"
## [1] "95.5056179775281 %"
## [1] "96.6292134831461 %"
## [1] "97.752808988764 %"
## [1] "98.876404494382 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

taxa = c(20:291) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.0989010989011 %"
## [1] "2.1978021978022 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "3.2967032967033 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.3956043956044 %"
## [1] "5.49450549450549 %"
## [1] "6.59340659340659 %"
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "8.79120879120879 %"
## [1] "9.89010989010989 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.989010989011 %"
## [1] "12.0879120879121 %"
## [1] "13.1868131868132 %"
## [1] "14.2857142857143 %"
## [1] "15.3846153846154 %"
## [1] "16.4835164835165 %"
## [1] "17.5824175824176 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.6813186813187 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.7802197802198 %"
## [1] "20.8791208791209 %"
## [1] "21.978021978022 %"
## [1] "23.0769230769231 %"
## [1] "24.1758241758242 %"
## [1] "25.2747252747253 %"
## [1] "26.3736263736264 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "27.4725274725275 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "28.5714285714286 %"
## [1] "29.6703296703297 %"
## [1] "30.7692307692308 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "31.8681318681319 %"
## [1] "32.967032967033 %"
## [1] "34.0659340659341 %"
## [1] "35.1648351648352 %"
## [1] "36.2637362637363 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "37.3626373626374 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "38.4615384615385 %"
## [1] "39.5604395604396 %"
## [1] "40.6593406593407 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "41.7582417582418 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.8571428571429 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "43.956043956044 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "45.0549450549451 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "47.2527472527472 %"
## [1] "48.3516483516484 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.4505494505495 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "50.5494505494505 %"
## [1] "51.6483516483517 %"
## [1] "52.7472527472528 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.8461538461538 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "54.9450549450549 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "56.043956043956 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.1428571428571 %"
## [1] "58.2417582417582 %"
## [1] "59.3406593406593 %"
## [1] "60.4395604395604 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.6373626373626 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.7362637362637 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "64.8351648351648 %"
## [1] "65.9340659340659 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "67.032967032967 %"
## [1] "68.1318681318681 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "70.3296703296703 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "71.4285714285714 %"
## [1] "72.5274725274725 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "73.6263736263736 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "74.7252747252747 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.8241758241758 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.9230769230769 %"
## [1] "78.021978021978 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.1208791208791 %"
## [1] "80.2197802197802 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "81.3186813186813 %"
## [1] "82.4175824175824 %"
## [1] "83.5164835164835 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "84.6153846153846 %"
## [1] "85.7142857142857 %"
## [1] "86.8131868131868 %"
## [1] "87.9120879120879 %"
## [1] "89.010989010989 %"
## [1] "90.1098901098901 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "91.2087912087912 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "93.4065934065934 %"
## [1] "94.5054945054945 %"
## [1] "95.6043956043956 %"
## [1] "96.7032967032967 %"
## [1] "97.8021978021978 %"
## [1] "98.9010989010989 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 2 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 2 rows containing non-finite values (stat_smooth).
## Warning: Removed 2 rows containing missing values (geom_point).

##TRIG

phe = c(6) #TRIG
# phe = c(7) #HDL
# phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:285) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.12359550561798 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "2.24719101123596 %"
## [1] "3.37078651685393 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.49438202247191 %"
## [1] "5.61797752808989 %"
## [1] "6.74157303370786 %"
## [1] "7.86516853932584 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "8.98876404494382 %"
## [1] "10.1123595505618 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "11.2359550561798 %"
## [1] "12.3595505617978 %"
## [1] "13.4831460674157 %"
## [1] "14.6067415730337 %"
## [1] "15.7303370786517 %"
## [1] "16.8539325842697 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "17.9775280898876 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.1011235955056 %"
## [1] "20.2247191011236 %"
## [1] "21.3483146067416 %"
## [1] "22.4719101123595 %"
## [1] "23.5955056179775 %"
## [1] "24.7191011235955 %"
## [1] "25.8426966292135 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.9662921348315 %"
## [1] "28.0898876404494 %"
## [1] "29.2134831460674 %"
## [1] "30.3370786516854 %"
## [1] "31.4606741573034 %"
## [1] "32.5842696629214 %"
## [1] "33.7078651685393 %"
## [1] "34.8314606741573 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "35.9550561797753 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "37.0786516853933 %"
## [1] "38.2022471910112 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3258426966292 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "40.4494382022472 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "41.5730337078652 %"
## [1] "42.6966292134831 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "43.8202247191011 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "44.9438202247191 %"
## [1] "46.0674157303371 %"
## [1] "47.1910112359551 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.314606741573 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.438202247191 %"
## [1] "50.561797752809 %"
## [1] "51.685393258427 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "52.8089887640449 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.9325842696629 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "55.0561797752809 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "56.1797752808989 %"
## [1] "57.3033707865169 %"
## [1] "58.4269662921348 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "59.5505617977528 %"
## [1] "60.6741573033708 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.7977528089888 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.9213483146067 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "64.0449438202247 %"
## [1] "65.1685393258427 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "66.2921348314607 %"
## [1] "67.4157303370787 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.5393258426966 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.6629213483146 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "70.7865168539326 %"
## [1] "71.9101123595506 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "73.0337078651685 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "74.1573033707865 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.2808988764045 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.4044943820225 %"
## [1] "77.5280898876404 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "78.6516853932584 %"
## [1] "79.7752808988764 %"
## [1] "80.8988764044944 %"
## [1] "82.0224719101124 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "83.1460674157303 %"
## [1] "84.2696629213483 %"
## [1] "85.3932584269663 %"
## [1] "86.5168539325843 %"
## [1] "87.6404494382023 %"
## [1] "88.7640449438202 %"
## [1] "89.8876404494382 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "91.0112359550562 %"
## [1] "92.1348314606742 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "93.2584269662921 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "94.3820224719101 %"
## [1] "95.5056179775281 %"
## [1] "96.6292134831461 %"
## [1] "97.752808988764 %"
## [1] "98.876404494382 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 73 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 73 rows containing non-finite values (stat_smooth).
## Warning: Removed 73 rows containing missing values (geom_point).

taxa = c(20:291) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.0989010989011 %"
## [1] "2.1978021978022 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "3.2967032967033 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.3956043956044 %"
## [1] "5.49450549450549 %"
## [1] "6.59340659340659 %"
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "8.79120879120879 %"
## [1] "9.89010989010989 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.989010989011 %"
## [1] "12.0879120879121 %"
## [1] "13.1868131868132 %"
## [1] "14.2857142857143 %"
## [1] "15.3846153846154 %"
## [1] "16.4835164835165 %"
## [1] "17.5824175824176 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.6813186813187 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.7802197802198 %"
## [1] "20.8791208791209 %"
## [1] "21.978021978022 %"
## [1] "23.0769230769231 %"
## [1] "24.1758241758242 %"
## [1] "25.2747252747253 %"
## [1] "26.3736263736264 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "27.4725274725275 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "28.5714285714286 %"
## [1] "29.6703296703297 %"
## [1] "30.7692307692308 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "31.8681318681319 %"
## [1] "32.967032967033 %"
## [1] "34.0659340659341 %"
## [1] "35.1648351648352 %"
## [1] "36.2637362637363 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "37.3626373626374 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "38.4615384615385 %"
## [1] "39.5604395604396 %"
## [1] "40.6593406593407 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "41.7582417582418 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.8571428571429 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "43.956043956044 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "45.0549450549451 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "47.2527472527472 %"
## [1] "48.3516483516484 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.4505494505495 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "50.5494505494505 %"
## [1] "51.6483516483517 %"
## [1] "52.7472527472528 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.8461538461538 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "54.9450549450549 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "56.043956043956 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.1428571428571 %"
## [1] "58.2417582417582 %"
## [1] "59.3406593406593 %"
## [1] "60.4395604395604 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.6373626373626 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.7362637362637 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "64.8351648351648 %"
## [1] "65.9340659340659 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "67.032967032967 %"
## [1] "68.1318681318681 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "70.3296703296703 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "71.4285714285714 %"
## [1] "72.5274725274725 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "73.6263736263736 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "74.7252747252747 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.8241758241758 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.9230769230769 %"
## [1] "78.021978021978 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.1208791208791 %"
## [1] "80.2197802197802 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "81.3186813186813 %"
## [1] "82.4175824175824 %"
## [1] "83.5164835164835 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "84.6153846153846 %"
## [1] "85.7142857142857 %"
## [1] "86.8131868131868 %"
## [1] "87.9120879120879 %"
## [1] "89.010989010989 %"
## [1] "90.1098901098901 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "91.2087912087912 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "93.4065934065934 %"
## [1] "94.5054945054945 %"
## [1] "95.6043956043956 %"
## [1] "96.7032967032967 %"
## [1] "97.8021978021978 %"
## [1] "98.9010989010989 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 88 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 88 rows containing non-finite values (stat_smooth).
## Warning: Removed 88 rows containing missing values (geom_point).

##HDL

phe = c(7) #HDL
# phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:285) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.12359550561798 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "2.24719101123596 %"
## [1] "3.37078651685393 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.49438202247191 %"
## [1] "5.61797752808989 %"
## [1] "6.74157303370786 %"
## [1] "7.86516853932584 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "8.98876404494382 %"
## [1] "10.1123595505618 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "11.2359550561798 %"
## [1] "12.3595505617978 %"
## [1] "13.4831460674157 %"
## [1] "14.6067415730337 %"
## [1] "15.7303370786517 %"
## [1] "16.8539325842697 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "17.9775280898876 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.1011235955056 %"
## [1] "20.2247191011236 %"
## [1] "21.3483146067416 %"
## [1] "22.4719101123595 %"
## [1] "23.5955056179775 %"
## [1] "24.7191011235955 %"
## [1] "25.8426966292135 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.9662921348315 %"
## [1] "28.0898876404494 %"
## [1] "29.2134831460674 %"
## [1] "30.3370786516854 %"
## [1] "31.4606741573034 %"
## [1] "32.5842696629214 %"
## [1] "33.7078651685393 %"
## [1] "34.8314606741573 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "35.9550561797753 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "37.0786516853933 %"
## [1] "38.2022471910112 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3258426966292 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "40.4494382022472 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "41.5730337078652 %"
## [1] "42.6966292134831 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "43.8202247191011 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "44.9438202247191 %"
## [1] "46.0674157303371 %"
## [1] "47.1910112359551 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.314606741573 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.438202247191 %"
## [1] "50.561797752809 %"
## [1] "51.685393258427 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "52.8089887640449 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.9325842696629 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "55.0561797752809 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "56.1797752808989 %"
## [1] "57.3033707865169 %"
## [1] "58.4269662921348 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "59.5505617977528 %"
## [1] "60.6741573033708 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.7977528089888 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.9213483146067 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "64.0449438202247 %"
## [1] "65.1685393258427 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "66.2921348314607 %"
## [1] "67.4157303370787 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.5393258426966 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.6629213483146 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "70.7865168539326 %"
## [1] "71.9101123595506 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "73.0337078651685 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "74.1573033707865 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.2808988764045 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.4044943820225 %"
## [1] "77.5280898876404 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "78.6516853932584 %"
## [1] "79.7752808988764 %"
## [1] "80.8988764044944 %"
## [1] "82.0224719101124 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "83.1460674157303 %"
## [1] "84.2696629213483 %"
## [1] "85.3932584269663 %"
## [1] "86.5168539325843 %"
## [1] "87.6404494382023 %"
## [1] "88.7640449438202 %"
## [1] "89.8876404494382 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "91.0112359550562 %"
## [1] "92.1348314606742 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "93.2584269662921 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "94.3820224719101 %"
## [1] "95.5056179775281 %"
## [1] "96.6292134831461 %"
## [1] "97.752808988764 %"
## [1] "98.876404494382 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 74 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 74 rows containing non-finite values (stat_smooth).
## Warning: Removed 74 rows containing missing values (geom_point).

taxa = c(20:291) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.0989010989011 %"
## [1] "2.1978021978022 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "3.2967032967033 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.3956043956044 %"
## [1] "5.49450549450549 %"
## [1] "6.59340659340659 %"
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "8.79120879120879 %"
## [1] "9.89010989010989 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.989010989011 %"
## [1] "12.0879120879121 %"
## [1] "13.1868131868132 %"
## [1] "14.2857142857143 %"
## [1] "15.3846153846154 %"
## [1] "16.4835164835165 %"
## [1] "17.5824175824176 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.6813186813187 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.7802197802198 %"
## [1] "20.8791208791209 %"
## [1] "21.978021978022 %"
## [1] "23.0769230769231 %"
## [1] "24.1758241758242 %"
## [1] "25.2747252747253 %"
## [1] "26.3736263736264 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "27.4725274725275 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "28.5714285714286 %"
## [1] "29.6703296703297 %"
## [1] "30.7692307692308 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "31.8681318681319 %"
## [1] "32.967032967033 %"
## [1] "34.0659340659341 %"
## [1] "35.1648351648352 %"
## [1] "36.2637362637363 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "37.3626373626374 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "38.4615384615385 %"
## [1] "39.5604395604396 %"
## [1] "40.6593406593407 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "41.7582417582418 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.8571428571429 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "43.956043956044 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "45.0549450549451 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "47.2527472527472 %"
## [1] "48.3516483516484 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.4505494505495 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "50.5494505494505 %"
## [1] "51.6483516483517 %"
## [1] "52.7472527472528 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.8461538461538 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "54.9450549450549 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "56.043956043956 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.1428571428571 %"
## [1] "58.2417582417582 %"
## [1] "59.3406593406593 %"
## [1] "60.4395604395604 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.6373626373626 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.7362637362637 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "64.8351648351648 %"
## [1] "65.9340659340659 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "67.032967032967 %"
## [1] "68.1318681318681 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "70.3296703296703 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "71.4285714285714 %"
## [1] "72.5274725274725 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "73.6263736263736 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "74.7252747252747 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.8241758241758 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.9230769230769 %"
## [1] "78.021978021978 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.1208791208791 %"
## [1] "80.2197802197802 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "81.3186813186813 %"
## [1] "82.4175824175824 %"
## [1] "83.5164835164835 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "84.6153846153846 %"
## [1] "85.7142857142857 %"
## [1] "86.8131868131868 %"
## [1] "87.9120879120879 %"
## [1] "89.010989010989 %"
## [1] "90.1098901098901 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "91.2087912087912 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "93.4065934065934 %"
## [1] "94.5054945054945 %"
## [1] "95.6043956043956 %"
## [1] "96.7032967032967 %"
## [1] "97.8021978021978 %"
## [1] "98.9010989010989 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 90 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 90 rows containing non-finite values (stat_smooth).
## Warning: Removed 90 rows containing missing values (geom_point).

##Systolic

phe = c(8) #Systolic
# phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:285) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.12359550561798 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "2.24719101123596 %"
## [1] "3.37078651685393 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.49438202247191 %"
## [1] "5.61797752808989 %"
## [1] "6.74157303370786 %"
## [1] "7.86516853932584 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "8.98876404494382 %"
## [1] "10.1123595505618 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "11.2359550561798 %"
## [1] "12.3595505617978 %"
## [1] "13.4831460674157 %"
## [1] "14.6067415730337 %"
## [1] "15.7303370786517 %"
## [1] "16.8539325842697 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "17.9775280898876 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.1011235955056 %"
## [1] "20.2247191011236 %"
## [1] "21.3483146067416 %"
## [1] "22.4719101123595 %"
## [1] "23.5955056179775 %"
## [1] "24.7191011235955 %"
## [1] "25.8426966292135 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.9662921348315 %"
## [1] "28.0898876404494 %"
## [1] "29.2134831460674 %"
## [1] "30.3370786516854 %"
## [1] "31.4606741573034 %"
## [1] "32.5842696629214 %"
## [1] "33.7078651685393 %"
## [1] "34.8314606741573 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "35.9550561797753 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "37.0786516853933 %"
## [1] "38.2022471910112 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3258426966292 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "40.4494382022472 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "41.5730337078652 %"
## [1] "42.6966292134831 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "43.8202247191011 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "44.9438202247191 %"
## [1] "46.0674157303371 %"
## [1] "47.1910112359551 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.314606741573 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.438202247191 %"
## [1] "50.561797752809 %"
## [1] "51.685393258427 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "52.8089887640449 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.9325842696629 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "55.0561797752809 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "56.1797752808989 %"
## [1] "57.3033707865169 %"
## [1] "58.4269662921348 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "59.5505617977528 %"
## [1] "60.6741573033708 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.7977528089888 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.9213483146067 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "64.0449438202247 %"
## [1] "65.1685393258427 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "66.2921348314607 %"
## [1] "67.4157303370787 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.5393258426966 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.6629213483146 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "70.7865168539326 %"
## [1] "71.9101123595506 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "73.0337078651685 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "74.1573033707865 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.2808988764045 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.4044943820225 %"
## [1] "77.5280898876404 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "78.6516853932584 %"
## [1] "79.7752808988764 %"
## [1] "80.8988764044944 %"
## [1] "82.0224719101124 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "83.1460674157303 %"
## [1] "84.2696629213483 %"
## [1] "85.3932584269663 %"
## [1] "86.5168539325843 %"
## [1] "87.6404494382023 %"
## [1] "88.7640449438202 %"
## [1] "89.8876404494382 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "91.0112359550562 %"
## [1] "92.1348314606742 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "93.2584269662921 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "94.3820224719101 %"
## [1] "95.5056179775281 %"
## [1] "96.6292134831461 %"
## [1] "97.752808988764 %"
## [1] "98.876404494382 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

taxa = c(20:291) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.0989010989011 %"
## [1] "2.1978021978022 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "3.2967032967033 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.3956043956044 %"
## [1] "5.49450549450549 %"
## [1] "6.59340659340659 %"
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "8.79120879120879 %"
## [1] "9.89010989010989 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.989010989011 %"
## [1] "12.0879120879121 %"
## [1] "13.1868131868132 %"
## [1] "14.2857142857143 %"
## [1] "15.3846153846154 %"
## [1] "16.4835164835165 %"
## [1] "17.5824175824176 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.6813186813187 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.7802197802198 %"
## [1] "20.8791208791209 %"
## [1] "21.978021978022 %"
## [1] "23.0769230769231 %"
## [1] "24.1758241758242 %"
## [1] "25.2747252747253 %"
## [1] "26.3736263736264 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "27.4725274725275 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "28.5714285714286 %"
## [1] "29.6703296703297 %"
## [1] "30.7692307692308 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "31.8681318681319 %"
## [1] "32.967032967033 %"
## [1] "34.0659340659341 %"
## [1] "35.1648351648352 %"
## [1] "36.2637362637363 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "37.3626373626374 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "38.4615384615385 %"
## [1] "39.5604395604396 %"
## [1] "40.6593406593407 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "41.7582417582418 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.8571428571429 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "43.956043956044 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "45.0549450549451 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "47.2527472527472 %"
## [1] "48.3516483516484 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.4505494505495 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "50.5494505494505 %"
## [1] "51.6483516483517 %"
## [1] "52.7472527472528 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.8461538461538 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "54.9450549450549 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "56.043956043956 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.1428571428571 %"
## [1] "58.2417582417582 %"
## [1] "59.3406593406593 %"
## [1] "60.4395604395604 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.6373626373626 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.7362637362637 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "64.8351648351648 %"
## [1] "65.9340659340659 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "67.032967032967 %"
## [1] "68.1318681318681 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "70.3296703296703 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "71.4285714285714 %"
## [1] "72.5274725274725 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "73.6263736263736 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "74.7252747252747 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.8241758241758 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.9230769230769 %"
## [1] "78.021978021978 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.1208791208791 %"
## [1] "80.2197802197802 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "81.3186813186813 %"
## [1] "82.4175824175824 %"
## [1] "83.5164835164835 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "84.6153846153846 %"
## [1] "85.7142857142857 %"
## [1] "86.8131868131868 %"
## [1] "87.9120879120879 %"
## [1] "89.010989010989 %"
## [1] "90.1098901098901 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "91.2087912087912 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "93.4065934065934 %"
## [1] "94.5054945054945 %"
## [1] "95.6043956043956 %"
## [1] "96.7032967032967 %"
## [1] "97.8021978021978 %"
## [1] "98.9010989010989 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

##Diastolic

phe = c(9) #Diastolic
# phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:285) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.12359550561798 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "2.24719101123596 %"
## [1] "3.37078651685393 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.49438202247191 %"
## [1] "5.61797752808989 %"
## [1] "6.74157303370786 %"
## [1] "7.86516853932584 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "8.98876404494382 %"
## [1] "10.1123595505618 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "11.2359550561798 %"
## [1] "12.3595505617978 %"
## [1] "13.4831460674157 %"
## [1] "14.6067415730337 %"
## [1] "15.7303370786517 %"
## [1] "16.8539325842697 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "17.9775280898876 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.1011235955056 %"
## [1] "20.2247191011236 %"
## [1] "21.3483146067416 %"
## [1] "22.4719101123595 %"
## [1] "23.5955056179775 %"
## [1] "24.7191011235955 %"
## [1] "25.8426966292135 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.9662921348315 %"
## [1] "28.0898876404494 %"
## [1] "29.2134831460674 %"
## [1] "30.3370786516854 %"
## [1] "31.4606741573034 %"
## [1] "32.5842696629214 %"
## [1] "33.7078651685393 %"
## [1] "34.8314606741573 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "35.9550561797753 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "37.0786516853933 %"
## [1] "38.2022471910112 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3258426966292 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "40.4494382022472 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "41.5730337078652 %"
## [1] "42.6966292134831 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "43.8202247191011 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "44.9438202247191 %"
## [1] "46.0674157303371 %"
## [1] "47.1910112359551 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.314606741573 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.438202247191 %"
## [1] "50.561797752809 %"
## [1] "51.685393258427 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "52.8089887640449 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.9325842696629 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "55.0561797752809 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "56.1797752808989 %"
## [1] "57.3033707865169 %"
## [1] "58.4269662921348 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "59.5505617977528 %"
## [1] "60.6741573033708 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.7977528089888 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.9213483146067 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "64.0449438202247 %"
## [1] "65.1685393258427 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "66.2921348314607 %"
## [1] "67.4157303370787 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.5393258426966 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.6629213483146 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "70.7865168539326 %"
## [1] "71.9101123595506 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "73.0337078651685 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "74.1573033707865 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.2808988764045 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.4044943820225 %"
## [1] "77.5280898876404 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "78.6516853932584 %"
## [1] "79.7752808988764 %"
## [1] "80.8988764044944 %"
## [1] "82.0224719101124 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "83.1460674157303 %"
## [1] "84.2696629213483 %"
## [1] "85.3932584269663 %"
## [1] "86.5168539325843 %"
## [1] "87.6404494382023 %"
## [1] "88.7640449438202 %"
## [1] "89.8876404494382 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "91.0112359550562 %"
## [1] "92.1348314606742 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "93.2584269662921 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "94.3820224719101 %"
## [1] "95.5056179775281 %"
## [1] "96.6292134831461 %"
## [1] "97.752808988764 %"
## [1] "98.876404494382 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

taxa = c(20:291) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.0989010989011 %"
## [1] "2.1978021978022 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "3.2967032967033 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.3956043956044 %"
## [1] "5.49450549450549 %"
## [1] "6.59340659340659 %"
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "8.79120879120879 %"
## [1] "9.89010989010989 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.989010989011 %"
## [1] "12.0879120879121 %"
## [1] "13.1868131868132 %"
## [1] "14.2857142857143 %"
## [1] "15.3846153846154 %"
## [1] "16.4835164835165 %"
## [1] "17.5824175824176 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.6813186813187 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.7802197802198 %"
## [1] "20.8791208791209 %"
## [1] "21.978021978022 %"
## [1] "23.0769230769231 %"
## [1] "24.1758241758242 %"
## [1] "25.2747252747253 %"
## [1] "26.3736263736264 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "27.4725274725275 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "28.5714285714286 %"
## [1] "29.6703296703297 %"
## [1] "30.7692307692308 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "31.8681318681319 %"
## [1] "32.967032967033 %"
## [1] "34.0659340659341 %"
## [1] "35.1648351648352 %"
## [1] "36.2637362637363 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "37.3626373626374 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "38.4615384615385 %"
## [1] "39.5604395604396 %"
## [1] "40.6593406593407 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "41.7582417582418 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.8571428571429 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "43.956043956044 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "45.0549450549451 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "47.2527472527472 %"
## [1] "48.3516483516484 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.4505494505495 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "50.5494505494505 %"
## [1] "51.6483516483517 %"
## [1] "52.7472527472528 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.8461538461538 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "54.9450549450549 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "56.043956043956 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.1428571428571 %"
## [1] "58.2417582417582 %"
## [1] "59.3406593406593 %"
## [1] "60.4395604395604 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.6373626373626 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.7362637362637 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "64.8351648351648 %"
## [1] "65.9340659340659 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "67.032967032967 %"
## [1] "68.1318681318681 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "70.3296703296703 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "71.4285714285714 %"
## [1] "72.5274725274725 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "73.6263736263736 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "74.7252747252747 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.8241758241758 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.9230769230769 %"
## [1] "78.021978021978 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.1208791208791 %"
## [1] "80.2197802197802 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "81.3186813186813 %"
## [1] "82.4175824175824 %"
## [1] "83.5164835164835 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "84.6153846153846 %"
## [1] "85.7142857142857 %"
## [1] "86.8131868131868 %"
## [1] "87.9120879120879 %"
## [1] "89.010989010989 %"
## [1] "90.1098901098901 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "91.2087912087912 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "93.4065934065934 %"
## [1] "94.5054945054945 %"
## [1] "95.6043956043956 %"
## [1] "96.7032967032967 %"
## [1] "97.8021978021978 %"
## [1] "98.9010989010989 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 1 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

##GLU

phe = c(10) #GLU
# phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:285) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.12359550561798 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "2.24719101123596 %"
## [1] "3.37078651685393 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.49438202247191 %"
## [1] "5.61797752808989 %"
## [1] "6.74157303370786 %"
## [1] "7.86516853932584 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "8.98876404494382 %"
## [1] "10.1123595505618 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "11.2359550561798 %"
## [1] "12.3595505617978 %"
## [1] "13.4831460674157 %"
## [1] "14.6067415730337 %"
## [1] "15.7303370786517 %"
## [1] "16.8539325842697 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "17.9775280898876 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.1011235955056 %"
## [1] "20.2247191011236 %"
## [1] "21.3483146067416 %"
## [1] "22.4719101123595 %"
## [1] "23.5955056179775 %"
## [1] "24.7191011235955 %"
## [1] "25.8426966292135 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.9662921348315 %"
## [1] "28.0898876404494 %"
## [1] "29.2134831460674 %"
## [1] "30.3370786516854 %"
## [1] "31.4606741573034 %"
## [1] "32.5842696629214 %"
## [1] "33.7078651685393 %"
## [1] "34.8314606741573 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "35.9550561797753 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "37.0786516853933 %"
## [1] "38.2022471910112 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3258426966292 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "40.4494382022472 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "41.5730337078652 %"
## [1] "42.6966292134831 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "43.8202247191011 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "44.9438202247191 %"
## [1] "46.0674157303371 %"
## [1] "47.1910112359551 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.314606741573 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.438202247191 %"
## [1] "50.561797752809 %"
## [1] "51.685393258427 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "52.8089887640449 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.9325842696629 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "55.0561797752809 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "56.1797752808989 %"
## [1] "57.3033707865169 %"
## [1] "58.4269662921348 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "59.5505617977528 %"
## [1] "60.6741573033708 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.7977528089888 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.9213483146067 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "64.0449438202247 %"
## [1] "65.1685393258427 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "66.2921348314607 %"
## [1] "67.4157303370787 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.5393258426966 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.6629213483146 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "70.7865168539326 %"
## [1] "71.9101123595506 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "73.0337078651685 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "74.1573033707865 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.2808988764045 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.4044943820225 %"
## [1] "77.5280898876404 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "78.6516853932584 %"
## [1] "79.7752808988764 %"
## [1] "80.8988764044944 %"
## [1] "82.0224719101124 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "83.1460674157303 %"
## [1] "84.2696629213483 %"
## [1] "85.3932584269663 %"
## [1] "86.5168539325843 %"
## [1] "87.6404494382023 %"
## [1] "88.7640449438202 %"
## [1] "89.8876404494382 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "91.0112359550562 %"
## [1] "92.1348314606742 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "93.2584269662921 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "94.3820224719101 %"
## [1] "95.5056179775281 %"
## [1] "96.6292134831461 %"
## [1] "97.752808988764 %"
## [1] "98.876404494382 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 74 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 74 rows containing non-finite values (stat_smooth).
## Warning: Removed 74 rows containing missing values (geom_point).

taxa = c(20:291) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.0989010989011 %"
## [1] "2.1978021978022 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "3.2967032967033 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.3956043956044 %"
## [1] "5.49450549450549 %"
## [1] "6.59340659340659 %"
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "8.79120879120879 %"
## [1] "9.89010989010989 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.989010989011 %"
## [1] "12.0879120879121 %"
## [1] "13.1868131868132 %"
## [1] "14.2857142857143 %"
## [1] "15.3846153846154 %"
## [1] "16.4835164835165 %"
## [1] "17.5824175824176 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.6813186813187 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.7802197802198 %"
## [1] "20.8791208791209 %"
## [1] "21.978021978022 %"
## [1] "23.0769230769231 %"
## [1] "24.1758241758242 %"
## [1] "25.2747252747253 %"
## [1] "26.3736263736264 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "27.4725274725275 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "28.5714285714286 %"
## [1] "29.6703296703297 %"
## [1] "30.7692307692308 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "31.8681318681319 %"
## [1] "32.967032967033 %"
## [1] "34.0659340659341 %"
## [1] "35.1648351648352 %"
## [1] "36.2637362637363 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "37.3626373626374 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "38.4615384615385 %"
## [1] "39.5604395604396 %"
## [1] "40.6593406593407 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "41.7582417582418 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.8571428571429 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "43.956043956044 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "45.0549450549451 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "47.2527472527472 %"
## [1] "48.3516483516484 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.4505494505495 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "50.5494505494505 %"
## [1] "51.6483516483517 %"
## [1] "52.7472527472528 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.8461538461538 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "54.9450549450549 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "56.043956043956 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.1428571428571 %"
## [1] "58.2417582417582 %"
## [1] "59.3406593406593 %"
## [1] "60.4395604395604 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.6373626373626 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.7362637362637 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "64.8351648351648 %"
## [1] "65.9340659340659 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "67.032967032967 %"
## [1] "68.1318681318681 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "70.3296703296703 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "71.4285714285714 %"
## [1] "72.5274725274725 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "73.6263736263736 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "74.7252747252747 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.8241758241758 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.9230769230769 %"
## [1] "78.021978021978 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.1208791208791 %"
## [1] "80.2197802197802 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "81.3186813186813 %"
## [1] "82.4175824175824 %"
## [1] "83.5164835164835 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "84.6153846153846 %"
## [1] "85.7142857142857 %"
## [1] "86.8131868131868 %"
## [1] "87.9120879120879 %"
## [1] "89.010989010989 %"
## [1] "90.1098901098901 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "91.2087912087912 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "93.4065934065934 %"
## [1] "94.5054945054945 %"
## [1] "95.6043956043956 %"
## [1] "96.7032967032967 %"
## [1] "97.8021978021978 %"
## [1] "98.9010989010989 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 90 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 90 rows containing non-finite values (stat_smooth).
## Warning: Removed 90 rows containing missing values (geom_point).

##GH

phe = c(11) #GH
# phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:285) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.12359550561798 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "2.24719101123596 %"
## [1] "3.37078651685393 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.49438202247191 %"
## [1] "5.61797752808989 %"
## [1] "6.74157303370786 %"
## [1] "7.86516853932584 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "8.98876404494382 %"
## [1] "10.1123595505618 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "11.2359550561798 %"
## [1] "12.3595505617978 %"
## [1] "13.4831460674157 %"
## [1] "14.6067415730337 %"
## [1] "15.7303370786517 %"
## [1] "16.8539325842697 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "17.9775280898876 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.1011235955056 %"
## [1] "20.2247191011236 %"
## [1] "21.3483146067416 %"
## [1] "22.4719101123595 %"
## [1] "23.5955056179775 %"
## [1] "24.7191011235955 %"
## [1] "25.8426966292135 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.9662921348315 %"
## [1] "28.0898876404494 %"
## [1] "29.2134831460674 %"
## [1] "30.3370786516854 %"
## [1] "31.4606741573034 %"
## [1] "32.5842696629214 %"
## [1] "33.7078651685393 %"
## [1] "34.8314606741573 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "35.9550561797753 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "37.0786516853933 %"
## [1] "38.2022471910112 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3258426966292 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "40.4494382022472 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "41.5730337078652 %"
## [1] "42.6966292134831 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "43.8202247191011 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "44.9438202247191 %"
## [1] "46.0674157303371 %"
## [1] "47.1910112359551 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.314606741573 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.438202247191 %"
## [1] "50.561797752809 %"
## [1] "51.685393258427 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "52.8089887640449 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.9325842696629 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "55.0561797752809 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "56.1797752808989 %"
## [1] "57.3033707865169 %"
## [1] "58.4269662921348 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "59.5505617977528 %"
## [1] "60.6741573033708 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.7977528089888 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.9213483146067 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "64.0449438202247 %"
## [1] "65.1685393258427 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "66.2921348314607 %"
## [1] "67.4157303370787 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.5393258426966 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.6629213483146 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "70.7865168539326 %"
## [1] "71.9101123595506 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "73.0337078651685 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "74.1573033707865 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.2808988764045 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.4044943820225 %"
## [1] "77.5280898876404 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "78.6516853932584 %"
## [1] "79.7752808988764 %"
## [1] "80.8988764044944 %"
## [1] "82.0224719101124 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "83.1460674157303 %"
## [1] "84.2696629213483 %"
## [1] "85.3932584269663 %"
## [1] "86.5168539325843 %"
## [1] "87.6404494382023 %"
## [1] "88.7640449438202 %"
## [1] "89.8876404494382 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "91.0112359550562 %"
## [1] "92.1348314606742 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "93.2584269662921 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "94.3820224719101 %"
## [1] "95.5056179775281 %"
## [1] "96.6292134831461 %"
## [1] "97.752808988764 %"
## [1] "98.876404494382 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 74 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 74 rows containing non-finite values (stat_smooth).
## Warning: Removed 74 rows containing missing values (geom_point).

taxa = c(20:291) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.0989010989011 %"
## [1] "2.1978021978022 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "3.2967032967033 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.3956043956044 %"
## [1] "5.49450549450549 %"
## [1] "6.59340659340659 %"
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "8.79120879120879 %"
## [1] "9.89010989010989 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.989010989011 %"
## [1] "12.0879120879121 %"
## [1] "13.1868131868132 %"
## [1] "14.2857142857143 %"
## [1] "15.3846153846154 %"
## [1] "16.4835164835165 %"
## [1] "17.5824175824176 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.6813186813187 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.7802197802198 %"
## [1] "20.8791208791209 %"
## [1] "21.978021978022 %"
## [1] "23.0769230769231 %"
## [1] "24.1758241758242 %"
## [1] "25.2747252747253 %"
## [1] "26.3736263736264 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "27.4725274725275 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "28.5714285714286 %"
## [1] "29.6703296703297 %"
## [1] "30.7692307692308 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "31.8681318681319 %"
## [1] "32.967032967033 %"
## [1] "34.0659340659341 %"
## [1] "35.1648351648352 %"
## [1] "36.2637362637363 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "37.3626373626374 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "38.4615384615385 %"
## [1] "39.5604395604396 %"
## [1] "40.6593406593407 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "41.7582417582418 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.8571428571429 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "43.956043956044 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "45.0549450549451 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "47.2527472527472 %"
## [1] "48.3516483516484 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.4505494505495 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "50.5494505494505 %"
## [1] "51.6483516483517 %"
## [1] "52.7472527472528 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.8461538461538 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "54.9450549450549 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "56.043956043956 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.1428571428571 %"
## [1] "58.2417582417582 %"
## [1] "59.3406593406593 %"
## [1] "60.4395604395604 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.6373626373626 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.7362637362637 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "64.8351648351648 %"
## [1] "65.9340659340659 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "67.032967032967 %"
## [1] "68.1318681318681 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "70.3296703296703 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "71.4285714285714 %"
## [1] "72.5274725274725 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "73.6263736263736 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "74.7252747252747 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.8241758241758 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.9230769230769 %"
## [1] "78.021978021978 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.1208791208791 %"
## [1] "80.2197802197802 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "81.3186813186813 %"
## [1] "82.4175824175824 %"
## [1] "83.5164835164835 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "84.6153846153846 %"
## [1] "85.7142857142857 %"
## [1] "86.8131868131868 %"
## [1] "87.9120879120879 %"
## [1] "89.010989010989 %"
## [1] "90.1098901098901 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "91.2087912087912 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "93.4065934065934 %"
## [1] "94.5054945054945 %"
## [1] "95.6043956043956 %"
## [1] "96.7032967032967 %"
## [1] "97.8021978021978 %"
## [1] "98.9010989010989 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Removed 90 rows containing non-finite values (stat_cor).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 90 rows containing non-finite values (stat_smooth).
## Warning: Removed 90 rows containing missing values (geom_point).

##AGE

phe = c(13) #AGE
# phe = c(14) #Waist


taxa = c(20:285) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.12359550561798 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "2.24719101123596 %"
## [1] "3.37078651685393 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.49438202247191 %"
## [1] "5.61797752808989 %"
## [1] "6.74157303370786 %"
## [1] "7.86516853932584 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "8.98876404494382 %"
## [1] "10.1123595505618 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "11.2359550561798 %"
## [1] "12.3595505617978 %"
## [1] "13.4831460674157 %"
## [1] "14.6067415730337 %"
## [1] "15.7303370786517 %"
## [1] "16.8539325842697 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "17.9775280898876 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.1011235955056 %"
## [1] "20.2247191011236 %"
## [1] "21.3483146067416 %"
## [1] "22.4719101123595 %"
## [1] "23.5955056179775 %"
## [1] "24.7191011235955 %"
## [1] "25.8426966292135 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.9662921348315 %"
## [1] "28.0898876404494 %"
## [1] "29.2134831460674 %"
## [1] "30.3370786516854 %"
## [1] "31.4606741573034 %"
## [1] "32.5842696629214 %"
## [1] "33.7078651685393 %"
## [1] "34.8314606741573 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "35.9550561797753 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "37.0786516853933 %"
## [1] "38.2022471910112 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3258426966292 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "40.4494382022472 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "41.5730337078652 %"
## [1] "42.6966292134831 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "43.8202247191011 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "44.9438202247191 %"
## [1] "46.0674157303371 %"
## [1] "47.1910112359551 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.314606741573 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.438202247191 %"
## [1] "50.561797752809 %"
## [1] "51.685393258427 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "52.8089887640449 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.9325842696629 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "55.0561797752809 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "56.1797752808989 %"
## [1] "57.3033707865169 %"
## [1] "58.4269662921348 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "59.5505617977528 %"
## [1] "60.6741573033708 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.7977528089888 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.9213483146067 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "64.0449438202247 %"
## [1] "65.1685393258427 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "66.2921348314607 %"
## [1] "67.4157303370787 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.5393258426966 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.6629213483146 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "70.7865168539326 %"
## [1] "71.9101123595506 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "73.0337078651685 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "74.1573033707865 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.2808988764045 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.4044943820225 %"
## [1] "77.5280898876404 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "78.6516853932584 %"
## [1] "79.7752808988764 %"
## [1] "80.8988764044944 %"
## [1] "82.0224719101124 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "83.1460674157303 %"
## [1] "84.2696629213483 %"
## [1] "85.3932584269663 %"
## [1] "86.5168539325843 %"
## [1] "87.6404494382023 %"
## [1] "88.7640449438202 %"
## [1] "89.8876404494382 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "91.0112359550562 %"
## [1] "92.1348314606742 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "93.2584269662921 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "94.3820224719101 %"
## [1] "95.5056179775281 %"
## [1] "96.6292134831461 %"
## [1] "97.752808988764 %"
## [1] "98.876404494382 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

taxa = c(20:291) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.0989010989011 %"
## [1] "2.1978021978022 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "3.2967032967033 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.3956043956044 %"
## [1] "5.49450549450549 %"
## [1] "6.59340659340659 %"
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "8.79120879120879 %"
## [1] "9.89010989010989 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.989010989011 %"
## [1] "12.0879120879121 %"
## [1] "13.1868131868132 %"
## [1] "14.2857142857143 %"
## [1] "15.3846153846154 %"
## [1] "16.4835164835165 %"
## [1] "17.5824175824176 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.6813186813187 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.7802197802198 %"
## [1] "20.8791208791209 %"
## [1] "21.978021978022 %"
## [1] "23.0769230769231 %"
## [1] "24.1758241758242 %"
## [1] "25.2747252747253 %"
## [1] "26.3736263736264 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "27.4725274725275 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "28.5714285714286 %"
## [1] "29.6703296703297 %"
## [1] "30.7692307692308 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "31.8681318681319 %"
## [1] "32.967032967033 %"
## [1] "34.0659340659341 %"
## [1] "35.1648351648352 %"
## [1] "36.2637362637363 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "37.3626373626374 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "38.4615384615385 %"
## [1] "39.5604395604396 %"
## [1] "40.6593406593407 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "41.7582417582418 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.8571428571429 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "43.956043956044 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "45.0549450549451 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "47.2527472527472 %"
## [1] "48.3516483516484 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.4505494505495 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "50.5494505494505 %"
## [1] "51.6483516483517 %"
## [1] "52.7472527472528 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.8461538461538 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "54.9450549450549 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "56.043956043956 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.1428571428571 %"
## [1] "58.2417582417582 %"
## [1] "59.3406593406593 %"
## [1] "60.4395604395604 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.6373626373626 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.7362637362637 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "64.8351648351648 %"
## [1] "65.9340659340659 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "67.032967032967 %"
## [1] "68.1318681318681 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "70.3296703296703 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "71.4285714285714 %"
## [1] "72.5274725274725 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "73.6263736263736 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "74.7252747252747 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.8241758241758 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.9230769230769 %"
## [1] "78.021978021978 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.1208791208791 %"
## [1] "80.2197802197802 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "81.3186813186813 %"
## [1] "82.4175824175824 %"
## [1] "83.5164835164835 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "84.6153846153846 %"
## [1] "85.7142857142857 %"
## [1] "86.8131868131868 %"
## [1] "87.9120879120879 %"
## [1] "89.010989010989 %"
## [1] "90.1098901098901 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "91.2087912087912 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "93.4065934065934 %"
## [1] "94.5054945054945 %"
## [1] "95.6043956043956 %"
## [1] "96.7032967032967 %"
## [1] "97.8021978021978 %"
## [1] "98.9010989010989 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

##Waist

phe = c(14) #Waist


taxa = c(20:285) #from merged.table_male
cor_table = multi_assoc(merged.table_male, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.12359550561798 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "2.24719101123596 %"
## [1] "3.37078651685393 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.49438202247191 %"
## [1] "5.61797752808989 %"
## [1] "6.74157303370786 %"
## [1] "7.86516853932584 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "8.98876404494382 %"
## [1] "10.1123595505618 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "11.2359550561798 %"
## [1] "12.3595505617978 %"
## [1] "13.4831460674157 %"
## [1] "14.6067415730337 %"
## [1] "15.7303370786517 %"
## [1] "16.8539325842697 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "17.9775280898876 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.1011235955056 %"
## [1] "20.2247191011236 %"
## [1] "21.3483146067416 %"
## [1] "22.4719101123595 %"
## [1] "23.5955056179775 %"
## [1] "24.7191011235955 %"
## [1] "25.8426966292135 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "26.9662921348315 %"
## [1] "28.0898876404494 %"
## [1] "29.2134831460674 %"
## [1] "30.3370786516854 %"
## [1] "31.4606741573034 %"
## [1] "32.5842696629214 %"
## [1] "33.7078651685393 %"
## [1] "34.8314606741573 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "35.9550561797753 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "37.0786516853933 %"
## [1] "38.2022471910112 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "39.3258426966292 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "40.4494382022472 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "41.5730337078652 %"
## [1] "42.6966292134831 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "43.8202247191011 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "44.9438202247191 %"
## [1] "46.0674157303371 %"
## [1] "47.1910112359551 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "48.314606741573 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.438202247191 %"
## [1] "50.561797752809 %"
## [1] "51.685393258427 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "52.8089887640449 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.9325842696629 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "55.0561797752809 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "56.1797752808989 %"
## [1] "57.3033707865169 %"
## [1] "58.4269662921348 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "59.5505617977528 %"
## [1] "60.6741573033708 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.7977528089888 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.9213483146067 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "64.0449438202247 %"
## [1] "65.1685393258427 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "66.2921348314607 %"
## [1] "67.4157303370787 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "68.5393258426966 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.6629213483146 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "70.7865168539326 %"
## [1] "71.9101123595506 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "73.0337078651685 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "74.1573033707865 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.2808988764045 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.4044943820225 %"
## [1] "77.5280898876404 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "78.6516853932584 %"
## [1] "79.7752808988764 %"
## [1] "80.8988764044944 %"
## [1] "82.0224719101124 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "83.1460674157303 %"
## [1] "84.2696629213483 %"
## [1] "85.3932584269663 %"
## [1] "86.5168539325843 %"
## [1] "87.6404494382023 %"
## [1] "88.7640449438202 %"
## [1] "89.8876404494382 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "91.0112359550562 %"
## [1] "92.1348314606742 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "93.2584269662921 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "94.3820224719101 %"
## [1] "95.5056179775281 %"
## [1] "96.6292134831461 %"
## [1] "97.752808988764 %"
## [1] "98.876404494382 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_male, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

taxa = c(20:291) #from merged.table_female
cor_table = multi_assoc(merged.table_female, taxa, phe, method = "spearman", run_ratio = FALSE, p.zeros = 0.5)
## [1] "1.0989010989011 %"
## [1] "2.1978021978022 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "3.2967032967033 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "4.3956043956044 %"
## [1] "5.49450549450549 %"
## [1] "6.59340659340659 %"
## [1] "7.69230769230769 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "8.79120879120879 %"
## [1] "9.89010989010989 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "10.989010989011 %"
## [1] "12.0879120879121 %"
## [1] "13.1868131868132 %"
## [1] "14.2857142857143 %"
## [1] "15.3846153846154 %"
## [1] "16.4835164835165 %"
## [1] "17.5824175824176 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "18.6813186813187 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "19.7802197802198 %"
## [1] "20.8791208791209 %"
## [1] "21.978021978022 %"
## [1] "23.0769230769231 %"
## [1] "24.1758241758242 %"
## [1] "25.2747252747253 %"
## [1] "26.3736263736264 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "27.4725274725275 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "28.5714285714286 %"
## [1] "29.6703296703297 %"
## [1] "30.7692307692308 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "31.8681318681319 %"
## [1] "32.967032967033 %"
## [1] "34.0659340659341 %"
## [1] "35.1648351648352 %"
## [1] "36.2637362637363 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "37.3626373626374 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "38.4615384615385 %"
## [1] "39.5604395604396 %"
## [1] "40.6593406593407 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "41.7582417582418 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "42.8571428571429 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "43.956043956044 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "45.0549450549451 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "46.1538461538462 %"
## [1] "47.2527472527472 %"
## [1] "48.3516483516484 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "49.4505494505495 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "50.5494505494505 %"
## [1] "51.6483516483517 %"
## [1] "52.7472527472528 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "53.8461538461538 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "54.9450549450549 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "56.043956043956 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "57.1428571428571 %"
## [1] "58.2417582417582 %"
## [1] "59.3406593406593 %"
## [1] "60.4395604395604 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "61.5384615384615 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "62.6373626373626 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "63.7362637362637 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "64.8351648351648 %"
## [1] "65.9340659340659 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "67.032967032967 %"
## [1] "68.1318681318681 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "69.2307692307692 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "70.3296703296703 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "71.4285714285714 %"
## [1] "72.5274725274725 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "73.6263736263736 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "74.7252747252747 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "75.8241758241758 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "76.9230769230769 %"
## [1] "78.021978021978 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties

## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "79.1208791208791 %"
## [1] "80.2197802197802 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "81.3186813186813 %"
## [1] "82.4175824175824 %"
## [1] "83.5164835164835 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "84.6153846153846 %"
## [1] "85.7142857142857 %"
## [1] "86.8131868131868 %"
## [1] "87.9120879120879 %"
## [1] "89.010989010989 %"
## [1] "90.1098901098901 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "91.2087912087912 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "92.3076923076923 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## [1] "93.4065934065934 %"
## [1] "94.5054945054945 %"
## [1] "95.6043956043956 %"
## [1] "96.7032967032967 %"
## [1] "97.8021978021978 %"
## [1] "98.9010989010989 %"
## Warning in cor.test.default(y, z, method = method): Cannot compute exact p-value
## with ties
## Warning: Setting row names on a tibble is deprecated.
plot = plot_comprsn(merged.table_female, cor_table, row = 1)
plot
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.

## Warning: Use of `data_tbl$zn` is discouraged. Use `zn` instead.
## `geom_smooth()` using formula 'y ~ x'

#Heatmap

#Male
# Visualizing the correlation in heatmap [30x30]; try with class x class- level 3
library(corrplot)
res = cor.mtest(merged.table_male[,c(5:11,13,14,20:285)], conf.level = 0.95, rm.na = T)
## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero
Correlation <- round(cor(merged.table_male[,c(5:11,13,14,20:285)],method = "spearman", use="complete.obs"), 2)
## Warning in cor(merged.table_male[, c(5:11, 13, 14, 20:285)], method =
## "spearman", : the standard deviation is zero
corrplot(Correlation, method = "ellipse", tl.col = "black", type = 'upper', tl.cex = 0.4, cl.cex = 0.4, p.mat = res$p, insig = "blank", sig.level = 0.05) #heatmap; blue=neg corr; red=pos corr
## Warning in corrplot(Correlation, method = "ellipse", tl.col = "black", type =
## "upper", : Not been able to calculate text margin, please try again with a clean
## new empty window using {plot.new(); dev.off()} or reduce tl.cex

#Female
# Visualizing the correlation in heatmap [30x30]; try with class x class- level 3
library(corrplot)
res = cor.mtest(merged.table_female[,c(5:11,13,14,20:291)], conf.level = 0.95, rm.na = T)
## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero

## Warning in cor(x, y): the standard deviation is zero
Correlation <- round(cor(merged.table_female[,c(5:11,13,14,20:291)],method = "spearman", use="complete.obs"), 2)
## Warning in cor(merged.table_female[, c(5:11, 13, 14, 20:291)], method =
## "spearman", : the standard deviation is zero
corrplot(Correlation, method = "ellipse", tl.col = "black", type = 'upper', tl.cex = 0.4, cl.cex = 0.4, p.mat = res$p, insig = "blank", sig.level = 0.05) #heatmap; blue=neg corr; red=pos corr
## Warning in corrplot(Correlation, method = "ellipse", tl.col = "black", type =
## "upper", : Not been able to calculate text margin, please try again with a clean
## new empty window using {plot.new(); dev.off()} or reduce tl.cex